Assessment of Popular DFT and Semiempirical Molecular Orbital Techniques for Calculating Relative Transition State Energies and Kinetic Product Distributions in Enantioselective Organocatalytic Reactions

Transesterification of Dimethyl Carbonate with Ethanol Catalyzed by Guanidine: A Theoretical Analysis

Density-functional theory (DFT) was performed to investigate the mechanistic features of different guanidine-based catalysts, namely, 1,1,3,3-tetramethyl guanidine (TMG) and 1,5,7-triaza-bicyclo-[4.4.0]dec-5-ene (TBD), for the transesterification reaction of dimethyl carbonate (DMC) with ethanol (EtOH). Different possible pathways were suggested in which these catalysts act as either nucleophile or base within a homogeneous system. The DFT results allowed not only the study of the thermochemistry aspects of all elementary reactions featured in the two different activation modes but also the accurate calculation of the free energy barriers for each case. Our findings showed that the catalyzed reaction proceeded through simultaneous activation of DMC and EtOH, facilitated by hydrogen bonding for both catalysts. This feature led to the formation of a stable intermediate with a relatively low free energy barrier. TBD exhibited a potentially more efficient mechanism, owing to its planar structure and dual-activation mode. The free energy barrier of the rate-limiting step, identified as the formation of a zwitterionic complex, then declined by approximately 50% when compared with the reaction without catalysts. Overall, the DFT approach provides good insight into the reactivity of both catalysts and helps to find possibilities for further enhancing the mechanistic features of both catalysts for this type of transesterification reaction.

Quantum Tunneling Instability in Pericyclic Reactions

Several cycloreversion reactions of the retro-Diels-Alder type were computationally assessed to understand their quantum tunneling (QT) reactivity. N2, CO, and other leaving groups were considered based on their strong exothermicity, as it reduces their thermodynamic and kinetic stabilities. Our results indicate that for many of these reactions, it is essential to take into account their QT decomposition rate, which can massively weaken their molecular stability and shorten their half-lives even at deep cryogenic temperatures. In practical terms, this indicates that many supposedly stable molecules will actually be unsynthesizable or unisolable, and therefore trying to prepare or detect them would be a futile attempt. In addition, we discuss the importance of tunneling to correctly understand the enthalpy of activation and the collective atomic effect on the tunneling kinetic isotope effects to test if third-row atoms can tunnel in a chemical reaction. This project raises the question of the importance of in silico chemistry to guide in vitro chemistry, especially in cases where the latter cannot solve its own uncertainties.

Temperature-Dependent Kinetics of the Reactions of the Criegee Intermediate CH2OO with Hydroxyketones

Though there is a growing body of literature on the kinetics of CIs with simple carbonyls, CI reactions with functionalized carbonyls such as hydroxyketones remain unexplored. In this work, the temperature-dependent kinetics of the reactions of CH2OO with two hydroxyketones, hydroxyacetone (AcOH) and 4-hydroxy-2-butanone (4H2B), have been studied using a laser flash photolysis transient absorption spectroscopy technique and complementary quantum chemistry calculations. Bimolecular rate constants were determined from CH2OO loss rates observed under pseudo-first-order conditions across the temperature range 275-335 K. Arrhenius plots were linear and yielded T-dependent bimolecular rate constants: kAcOH(T) = (4.3 ± 1.7) × 10-15 exp[(1630 ± 120)/T] and k4H2B(T) = (3.5 ± 2.6) × 10-15 exp[(1700 ± 200)/T]. Both reactions show negative temperature dependences and overall very similar rate constants. Stationary points on the reaction energy surfaces were characterized using the composite CBS-QB3 method. Transition states were identified for both 1,3-dipolar cycloaddition reactions across the carbonyl and 1,2-insertion/addition at the hydroxyl group. The free-energy barriers for the latter reaction pathways are higher by ∼4-5 kcal mol-1, and their contributions are presumed to be negligible for both AcOH and 4H2B. The cycloaddition reactions are highly exothermic and form cyclic secondary ozonides that are the typical primary products of Criegee intermediate reactions with carbonyl compounds. The reactivity of the hydroxyketones toward CH2OO appears to be similar to that of acetaldehyde, which can be rationalized by consideration of the energies of the frontier molecular orbitals involved in the cycloaddition. The CH2OO + hydroxyketone reactions are likely too slow to be of significance in the atmosphere, except at very low temperatures.

Mechanism of Action of Antitumor Au(I) N-Heterocyclic Carbene Complexes: A Computational Insight on the Targeting of TrxR Selenocysteine

The targeting of human thioredoxin reductase is widely recognized to be crucially involved in the anticancer properties of several metallodrugs, including Au(I) complexes. In this study, the mechanism of reaction between a set of five N-heterocyclic carbene Au(I) complexes and models of the active Sec residue in human thioredoxin reductase was investigated by means of density functional theory approaches. The study was specifically addressed to the kinetics and thermodynamics of the tiled process by aiming at elucidating and explaining the differential inhibitory potency in this set of analogous Au(I) bis-carbene complexes. While the calculated free energy profile showed a substantially similar reactivity, we found that the binding of these Au(I) bis-carbene at the active CysSec dyad in the TrxR enzyme could be subjected to steric and orientational restraints, underlining both the approach of the bis-carbene scaffold and the attack of the selenol group at the metal center. A new and detailed mechanistic insight to the anticancer activity of these Au(I) organometallic complexes was thus provided by consolidating the TrxR targeting paradigm.

Theoretical Prediction of the Reaction Probabilities of H, O, and OH Radicals on the Polypropylene Surface

To determine the H-abstraction reaction probabilities of H/O/OH radicals with a polypropylene (PP) surface, a first-principles calculation was performed based on the DLPNO-CCSD(T)/CBS//M06-2X-D3/def-TZVP theory level. The PP chain model used in this study was 2,4,6-trimethylheptane. The rate constants of the H/O/OH radicals with the isolated PP chain model were calculated based on the conventional transition-state theory. By comparing the experimental values and considering the error factors and their compensation, it was concluded that the orders of magnitude of the predicted rate constants were accurate. The resulting rate constants were converted to reaction probabilities between the H/O/OH radicals and the PP surface. The method used in this study is applicable for obtaining theoretical values of surface reaction probabilities based on first-principles calculations. The calculation at the DLPNO-CCSD(T)/CBS theory level has high accuracy but consumes a large amount of computational resources. The study also demonstrated that the double-hybrid functionals, wB97x-2-D3(BJ) and rev-DSD-PBEP86-D3(BJ), with a 3-ζ or 4-ζ basis set, could reproduce the electronic energy values obtained from DLPNO-CCSD(T)/CBS while using only approximately 1/100 of the computational resources required by the latter under our computer configuration.

A Computational Exploration of Exohedrally Transition Metal Doped Si94- Superatom Based Magnetic MSi9M' Clusters (M, M' = Sc(II) to Cu(II))

Nanosized clusters are drawing immense attention of the scientific community due to their size and composition dependent tunability of physical and chemical properties. Silicon nanoclusters are especially important because of their abundance and ample utility in the domains of electronics and semiconductor industry. Zintl phases of Si offer an excellent opportunity in the domain of nanocluster research owing to their superior stability and multifarious possibilities of tunability of electronic properties through doping with other elements. Doping silicon clusters with transition elements is a prevalent strategy to induce magnetic properties in such clusters. Although doping silicon clusters with single transition metal atoms can induce significant magnetism in nanoclusters, the dominant covalent interaction between silicon and the transition metal causes the magnetic moment to quench. The rational strategy of inducing a sustainable magnetic moment can be to introduce ferromagnetic interaction between two sites carrying nonvanishing magnetic moments. In the present work, such a possibility is explored in terms of the stability of the clusters and corresponding magnetic exchange coupling in them. The Si94-superatomic cluster is doped with two transition metal atoms exohedrally and the neutral clusters designed thereby are investigated computationally if they reduce or reinforce the high stability of the superatom and substantiate the possibility of obtaining nanosized magnetic units as building blocks of tunable materials for various applications.

A brand-new type of excited-state proton transfer (ESIPT) molecule based on sulfoxide/sulfenic acid tautomerism

The excited-state proton transfer (ESIPT) behavior of organic fluorophores has attracted much attention due to their unique photophysical properties. So far, ESIPT studies have mainly focused on the transfer of hydrogen atoms between N-N, N-O, or O-O. In this work, a brand-new type of ESIPT molecule based on sulfoxide/sulfenic acid tautomerism has been thoroughly investigated. The sulfoxide/sulfenic acid tautomerization process requires one step and two steps in the ground and first excited singlet states, respectively. A range of density functional theory and time-dependent density functional theory methods have been employed to investigate these structures, and the changes in aromaticity may be responsible for obtaining the ESIPT process. This work presents a novel ESIPT process, showcasing molecules that exhibit distinctive properties compared to conventional ESIPT compounds. These findings are expected to expand the horizons of experimental research in ESIPT.

Generation of broad-spectrum recombinant antibody and construction of colorimetric immunoassay for tropane alkaloids: Recognition mechanism and application

Tropane alkaloids (TAs) have emerged as plant toxins, related to poisoning events. The development of stable antibodies is crucial to ensure the effectiveness of immunological methods in quickly and accurately monitoring these alkaloids. In this study, based on hybridoma, the variable region gene of monoclonal antibody (mAb) was amplified, and the recombinant antibody (rAb) gene sequence (VH-Linker-VL) was successfully constructed and expressed in HEK293F. The obtained rAb has kept the same performance as mAb, and the IC50 of 29 TAs ranged from 0.12 to 2642.78 ng/mL. In the recognition mechanism, the docking and dynamics model identified hydrophobic interaction as the most critical force. Substituent will impact recognition by influencing the spatial structure and hydrophobic properties. Then, a colorimetric immunoassay based on rAb was established, five types of water and thirty-nine nectars of honey were tested. The results demonstrated the absence of TAs in environmental water, whereas atropine was detected in more than 13.47% of honey samples at concentrations exceeding 1 μg/kg. The results show a good correlation with UHPLC-MS/MS, suggesting that the immunoassay has excellent screening ability. The data on TAs in honey and water could serve as a foundation for developing relevant policies.

Site-Averaged Ab Initio Kinetics: Importance Learning for Multistep Reactions on Amorphous Supports

Single-atom centers on amorphous supports include catalysts for polymerization, partial oxidation, metathesis, hydrogenolysis, and more. The disordered environment makes each site different, and the kinetics exponentially magnifies these differences to make ab initio site-averaged kinetics calculations extremely difficult. This work extends the importance learning algorithm for efficient and precise site-averaged kinetics estimates to ab initio calculations and multistep reaction mechanisms. Specifically, we calculate site-averaged proton transfer relaxation rates on an ensemble of cluster models representing Brønsted acid sites on silica-alumina. We include direct and water-assisted proton transfer pathways and simultaneously estimate the water adsorption and activation enthalpies for forward and backward proton transfers. We use density functional theory (DFT) to obtain a site-averaged rate, somewhat like a turnover frequency, for the proton transfer relaxation rate. Finally, we show that importance learning can provide orders-of-magnitude acceleration over standard sampling methods for site-averaged rate calculations in cases where the rate is dominated by a few highly active sites.

The performance of exchange-correlation functionals in describing electron density parameters of saddle point structures along chemical reactions

This work is focused on evaluating the performance of exchange-correlation functionals from density functional theory in providing descriptor values derived from the electron density of saddle point structures (transition states) in chemical reactions. The properties investigated were obtained from the quantum theory of atoms in molecules, including atomic charges and electron density topological data at the bond critical points. In addition, parameters from the Interacting quantum atom energy partition were used as well in this comparative study. The reference values are attained in coupled cluster calculations with iterative single and double excitations (CCSD). Six elementary reactions are considered here: CO + H₂  ↔ H₂ CO, CO + H₂ O ↔ HCOOH, HCN ↔ HNC, H + F₂  ↔ HF + F, H + N₂  ↔ HN₂ , and H + CO ↔ HCO. In general, the BB1K functional (hybrid-meta-generalized gradient approximation) provides the best description of these properties. Our study indicates that an intermediate percentage of nonlocal exact exchange, around 40%-55% (perhaps even larger), is probably required for attaining more accurate values with actual functionals, although this condition is not able of explaining all the trends observed.

Kinetic and Mechanistic Investigations of OH-Initiated Atmospheric Degradation of Methyl Butyl Ketone

Methyl butyl ketone (MBK, 2-hexanone) is a common atmospheric oxygenated volatile organic compound (OVOC) owing to broad industrial applications, but its atmospheric oxidation mechanism remains poorly understood. Herein, the detailed mechanisms and kinetic properties of MBK oxidation initiated by OH radicals and subsequent transformation of the resulting intermediates are performed by employing quantum chemical and kinetic modeling methods. The calculations show that H-abstraction at the C4 position of MBK is more favorable than those at the other positions, with the total rate coefficient of k(T) = 4.13 × 10^-14 exp(1576/T) cm³ molecule^-1 s^-1 at 273-400 K. The dominant pathway of unimolecular degradation of the C-centered alkyl radical is 1,2-acyl group migration. For the isomerization of the peroxy radical RO₂, 1,5- and 1,6-H shifts are more favorable than 1,3- and 1,4-H shifts. The multiconformer rate coefficient k_MC-TST of the first H-shift of the RO₂ radical is estimated to be 1.40 × 10^-3 s^-1 at room temperature. Compared to the H-shifts of analogous aliphatic RO₂ radicals, it can be concluded that the carbonyl group enhances the H-shift rates by as much as 2-4 orders of magnitude. The rate coefficients of the RO₂ radical reaction with the HO₂ radical exhibit a weakly negative temperature dependence, and the pseudo-first-order rate constant k'_HO2 = k_HO2[HO₂] is calculated to be 3.32-22.10 × 10^-3 s^-1 at ambient temperature. The bimolecular reaction of the RO₂ radical with NO leads to the formation of 3-oxo-butanal as the main product with the formation concentration of 2.2-7.4 μg/m³ in urban areas. The predicted pseudo-first-order rate constant k'_NO = k_NO[NO] is 2.20-9.98 s^-1 at room temperature. By comparing the k_MC-TST, k'_HO2, and k'_NO, it can be concluded that reaction with NO is the dominant removal pathway for the RO₂ radical formed from the OH-initiated oxidation of MBK. These findings are expected to deepen our understanding of the photochemical oxidation of ketones under realistic atmospheric conditions.

Competing pathways of cresol formation in toluene photooxidation: OH-toluene adducts react with NO2 or with O2?

Methyl-hydroxy-cyclohexadienyl radicals (OTAs) are the key products of the photooxidation of toluene, with implications for the fate of toluene. Hence, we investigated the photooxidation mechanisms and kinetics of three main OTAs (o-OTA, m-OTA, and p-OTA) with NO₂ using quantum chemical calculations as well as the fate of OTAs under the different concentration ratios of NO₂ and O₂. The mechanism results show that the pathway of H-abstraction by NO₂ to anti-HONO (anti-H-abstraction) is more favorable than the syn-H-abstraction pathway, because the strong interaction between OTAs and NO₂ is formed in the transition states of the anti-H-abstraction pathways. The branching ratios of the anti-H-abstraction pathways are more than 99% in the temperature range of 216-298 K. The total rate constant of the OTA-NO₂ reaction is 9.9 × 10^-12 cm³/(molecule∙sec) at 298 K, which is contributed about 90% by o-OTA + NO₂, and the main products are o-cresol and anti-HONO. The half-lives of the OTA-NO₂ reaction in some polluted areas of China are 35 times longer than those of the OTA-O₂ reaction. In the atmosphere, the NO₂- and O₂- initiated reactions of OTAs have the same ability to form cresols as [NO₂] is up to 142.1 ppmV, which is impossible to achieve. It implies that under the experimental condition, the [NO₂]/[O₂] should be controlled to be less than 7.8 × 10^-5 to simulate real atmospheric oxidation of toluene. Our results reveal that for the photooxidation of toluene, the yield of cresol is not affected by the concentration of NO₂ under the atmospheric environment.

Multifunctional Oxazolone Derivative as an Optical Amplifier, Generator, and Modulator

An optical control of many working optoelectronic systems (real-time sensors, optical modulators, light amplifiers, or phase retarders) giving efficient optical gain or remote signal modulation is currently included as scientifically and industrially interesting. In here, an oxazolone derivative as the multifunctional organic system is given in this contribution. The molecule possesses a stilbene group and an oxazolone heteroatomic ring, which implies effective refractive index manipulation and multimode lasing action, respectively. The light modulation is repeatable and stable, also in the hundreds of Hz regime. On the other hand, the amplified optical signal can be easily generated by an external optical pumping source. Thus, signal control is fully available, as is read-in and read-out of the information in real time. Furthermore, this third-order, nonlinear, optical phenomenon using a third harmonic generation technique was also observed. We discovered that only by changing the energy and time regime of the supplied optical signal is the optical or nonlinear optical response observed. Two heteroenergetic molecular states (trans (E) and cis (Z)) can efficiently operate in modern multifunctional optoelectronic systems, which can provide and generate an optical signal. Such functionalities are commonly used in all-optical photonic switchers and logic gates and can be utilized in optical-core networks and computers.

Kinetics of the Reactions of CH2OO with Acetone, α-Diketones, and β-Diketones

Rate constants for the reactions between the simplest Criegee intermediate, CH₂OO, with acetone, the α-diketones biacetyl and acetylpropionyl, and the β-diketones acetylacetone and 3,3-dimethyl-2,4-pentanedione have been measured at 295 K. CH₂OO was produced photochemically in a flow reactor by 355 nm laser flash photolysis of diiodomethane in the presence of excess oxygen. Time-dependent concentrations were measured using broadband transient absorption spectroscopy, and the reaction kinetics was characterized under pseudo-first-order conditions. The bimolecular rate constant for the CH₂OO + acetone reaction is measured to be (4.1 ± 0.4) × 10^-13 cm³ s^-1, consistent with previous measurements. The reactions of CH₂OO with the β-diketones acetylacetone and 3,3-dimethyl-2,5-pentanedione are found to have broadly similar rate constants of (6.6 ± 0.7) × 10^-13 and (3.5 ± 0.8) × 10^-13 cm³ s^-1, respectively; these values may be cautiously considered as upper limits. In contrast, α-diketones react significantly faster, with rate constants of (1.45 ± 0.18) × 10^-11 and (1.29 ± 0.15) × 10^-11 cm³ s^-1 measured for biacetyl and acetylpropionyl. The potential energy surfaces for these 1,3-dipolar cycloaddition reactions are characterized at the M06-2X/aug-cc-pVTZ and CBS-QB3 levels of theory and provide additional support to the observed experimental trends. The reactivity of carbonyl compounds with CH₂OO is also interpreted by application of frontier molecular orbital theory and predicted using Hammett substituent constants. Finally, the results are compared with other kinetic studies of Criegee intermediate reactions with carbonyl compounds and discussed within the context of their atmospheric relevance.

Connecting Gas-Phase Computational Chemistry to Condensed Phase Kinetic Modeling: The State-of-the-Art

In recent decades, quantum chemical calculations (QCC) have increased in accuracy, not only providing the ranking of chemical reactivities and energy barriers (e.g., for optimal selectivities) but also delivering more reliable equilibrium and (intrinsic/chemical) rate coefficients. This increased reliability of kinetic parameters is relevant to support the predictive character of kinetic modeling studies that are addressing actual concentration changes during chemical processes, taking into account competitive reactions and mixing heterogeneities. In the present contribution, guidelines are formulated on how to bridge the fields of computational chemistry and chemical kinetics. It is explained how condensed phase systems can be described based on conventional gas phase computational chemistry calculations. Case studies are included on polymerization kinetics, considering free and controlled radical polymerization, ionic polymerization, and polymer degradation. It is also illustrated how QCC can be directly linked to material properties.

A theoretical investigation on the atmospheric degradation of the radical: reactions with NO, NO2, and NO3

The radical is the key intermediate in the atmospheric oxidation of benzaldehyde, and its further chemistry contributes to local air pollution. The reaction mechanisms of the radical with NO, NO₂, and NO₃ were studied by quantum chemistry calculations at the CCSD(T)/CBS//M06-2X/def2-TZVP level of theory. The explicit potential energy curves were provided in order to reveal the atmospheric fate of the radical comprehensively. The main products of the reaction of with NO are predicted to be , CO₂ and NO₂. The reaction of with NO₂ is reversible, and its main product would be C₆H₅C(O)O₂NO₂ which was predicted to be more stable than PAN (peroxyacetyl nitrate) at room temperature. The decomposition of C₆H₅C(O)O₂NO₂ at different ambient temperatures would be a potential long-range transport source of NO_x in the atmosphere. The predominant products of the reaction are predicted to be C₆H₅C(O)O₂H, C₆H₅C(O)OH, O₂ and O₃, while HO˙ is of minor importance. So, the reaction of with would be an important source of ozone and carboxylic acids in the local atmosphere, and has less contribution to the regeneration of HO˙ radicals. The reaction of with NO₃ should mainly produce , CO₂, O₂ and NO₂, which might play an important role in atmospheric chemistry of peroxy radicals at night, but has less contribution to the night-time conversion of ( and RO˙) to ( and HO˙) in the local atmosphere. The results above are in good accordance with the reported experimental observations.

On the Mechanism of the Asymmetric Aldol Addition of Chiral N-Amino Cyclic Carbamate Hydrazones: Evidence of Non-Curtin-Hammett Behavior

he mechanistic details of the aldol addition of N-amino cyclic carbamate (ACC) hydrazones is provided herein from both an experimental and computational perspective. When the transformation is carried out at room temperature the anti-aldol product is formed exclusively. Under these conditions the anti- and syn-aldolate intermediates are in equilibrium and the transformation is under thermodynamic control. The anti-aldolate that leads to the anti-aldol product was calculated to be 3.7 kcal mol^-1 lower in energy at room temperature than that leading to the syn-aldol product, which sufficiently accounts for the exclusive formation of the anti-aldol product. When the reaction is conducted at -78 °C it is under kinetic control and favors formation of the syn-aldol addition product. In this case, it was found that a solvent separated aza-enolate anion and aldehyde form a σ-intermediate in which the lithium cation is coordinated to the aldehyde. The σ-intermediate collapses with a very small activation barrier to form the β-alkoxy hydrazone intermediate. The chiral nonracemic lithium aza-enolate discriminates between the two diastereotopic faces of the pro-chiral aldehyde, and there is no rapid direct pathway that interconverts the two diastereomeric intermediates. Consequently, the reaction does not follow the Curtin-Hammett principle and the stereochemical outcome at low temperature instead depends on the relative energies of the two σ-intermediates.

Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations

The C-terminus domain of non-structural 3 (NS3) protein of the Flaviviridae viruses (e.g. HCV, dengue, West Nile, Zika) is a nucleotide triphosphatase (NTPase) -dependent superfamily 2 (SF2) helicase that unwinds double-stranded RNA while translocating along the nucleic polymer. Due to these functions, NS3 is an important target for antiviral development yet the biophysics of this enzyme are poorly understood. Microsecond-long molecular dynamic simulations of the dengue NS3 helicase domain are reported from which allosteric effects of RNA and NTPase substrates are observed. The presence of a bound single-stranded RNA catalytically enhances the phosphate hydrolysis reaction by affecting the dynamics and positioning of waters within the hydrolysis active site. Coupled with results from the simulations, electronic structure calculations of the reaction are used to quantify this enhancement to be a 150-fold increase, in qualitative agreement with the experimental enhancement factor of 10–100. Additionally, protein-RNA interactions exhibit NTPase substrate-induced allostery, where the presence of a nucleotide (e.g. ATP or ADP) structurally perturbs residues in direct contact with the phosphodiester backbone of the RNA. Residue-residue network analyses highlight pathways of short ranged interactions that connect the two active sites. These analyses identify motif V as a highly connected region of protein structure through which energy released from either active site is hypothesized to move, thereby inducing the observed allosteric effects. These results lay the foundation for the design of novel allosteric inhibitors of NS3.

Non-structural protein 3 (NS3) is a Flaviviridae (e.g. Hepatitis C, dengue, and Zika viruses) helicase that unwinds double stranded RNA while translocating along the nucleic polymer during viral genome replication. As a member of superfamily 2 (SF2) helicases, NS3 utilizes the free energy of nucleotide triphosphate (NTP) binding, hydrolysis, and product unbinding to perform its functions. While much is known about SF2 helicases, the pathways and mechanisms through which free energy is transduced between the NTP hydrolysis active site and RNA binding cleft remains elusive. Here we present a multiscale computational study to characterize the allosteric effects induced by the RNA and NTPase substrates (ATP, ADP, and P_i) as well as the pathways of short-range, residue-residue interactions that connect the two active sites. Results from this body of molecular dynamics simulations and electronic structure calculations are highlighted in context to the NTPase enzymatic cycle, allowing for development of testable hypotheses for validation of these simulations. Our insights, therefore, provide novel details about the biophysics of NS3 and guide the next generation of experimental studies.

Computing organic stereoselectivity - from concepts to quantitative calculations and predictions

Advances in theory and processing power have established computation as a valuable interpretative and predictive tool in the discovery of new asymmetric catalysts. This tutorial review outlines the theory and practice of modeling stereoselective reactions. Recent examples illustrate how an understanding of the fundamental principles and the application of state-of-the-art computational methods may be used to gain mechanistic insight into organic and organometallic reactions. We highlight the emerging potential of this computational tool-box in providing meaningful predictions for the rational design of asymmetric catalysts. We present an accessible account of the field to encourage future synergy between computation and experiment.

On the asymmetric autocatalysis of aldol reactions: The case of 4-nitrobenzaldehyde and acetone. A critical appraisal with a focus on theory

Under neutral conditions, spontaneous mirror symmetry breaking has been occasionally reported for aldol reactions starting from achiral reagents and conditions. Chiral induction might be interpreted in terms of autocatalysis exerted by chiral mono-aldol or bis-aldol products as source of initial enantiomeric excesses, which may account for such experimental observations. We describe here a thorough Density Functional Theory (DFT) study on this complex and otherwise difficult problem, which provides some insights into this phenomenon. The picture adds further rationale to an in-depth analysis by Moyano et al, who showed the isolation and characterization of bis-aldol adducts and their participation in a complex network of reversible steps. However, the lack of enantiodiscrimination (ees vanish rapidly in solution) suggests, according to the present results, a weak association in complexes formed by the catalysts and substrates. The latter would also be consistent with almost flat transition states having similar heights for competitive catalyst-bound transition structures (actually, we were unable to locate them at the level explored). Overall, neither autocatalysis as once conjectured nor mutual inhibition of enantiomers appears to be operating mechanisms. Asymmetric amplification in early stages harnessing unavoidable enantiomeric imbalances in reaction mixtures of chiral products represents a plausible interpretation.

Unveiling the role of boroxines in metal-free carbon-carbon homologations using diazo compounds and boronic acids

By means of computational and experimental mechanistic studies the fundamental role of boroxines in the reaction between diazo compounds and boronic acids was elucidated.

By means of computational and experimental mechanistic studies the fundamental role of boroxines in the reaction between diazo compounds and boronic acids was elucidated. Consequently, a selective metal-free carbon–carbon homologation of aryl and vinyl boroxines using TMSCHN₂, giving access to TMS-pinacol boronic ester products, was developed.

Cooperativity of axial and centre chirality in the biaryl disulfoxide/Rh(i)-catalysed asymmetric 1,4-addition of arylboronic aids to 2-cyclohexenone: a DFT study

Atropisomeric biaryl disulfoxides contain two independent chiral elements. Previously, the (M,S,S)-diastereomer showed very high catalytic activity and selectivity in the Rh-catalyzed asymmetric 1,4-addition of arylboronic acids to α,β-enones whereas the (M,R,R) counterpart - none. Herein, DFT computations on the key transmetallation (turnover-determining) and carborhodation (enantioselectivity-determining) steps of the catalytic cycle show that the (M,S,S)-ligand gives rise to lower reaction barriers for these elementary steps. However, the barriers for the (M,R,R)-ligand are not sufficiently high to explain the lack of reactivity. Hence, this phenomenon is most likely due to the failure of catalyst formation from the ligand and the dimeric Rh precatalyst complex. The hitherto unknown (M,S,R)-ligand shows predicted enantioselectivity similar to the (M,S,S)-ligand as a consequence of lower reaction barriers associated with those isomers whose key features resemble the (M,S,S)-ligand.

Experimental and Quantum Mechanical Study of Nucleophilic Substitution Reactions of meta- and para-Substituted Benzyl Bromides with Benzylamine in Methanol: Synergy Between Experiment and Theory

This work involves the experimental and theoretical study of the nucleophilic substitution of meta- and para-substituted benzyl bromides with benzylamine. Conductometric rate experiments confirm the applicability of the Hammett linear free-energy relationship to this system. To gain a deep understanding of the physical chemistry at play, a quantum mechanical study of the reaction is also conducted. The quantum mechanical calculations not only reproduce the experimental free energy of activation, but also provide greater insights at the molecular and atomic level. Isolation of the calculated transition state structure and application of the Hammett equation to its electronic, structural, and energetic properties are studied.

Guanidine-catalyzed asymmetric Strecker reaction: modes of activation and origin of stereoselectivity

Density functional theory calculations were employed to study the catalytic mechanism, modes of activation, and origin of enantioselectivity of guanidine-catalyzed asymmetric Strecker reaction of N-benzhydryl imine with hydrogen cyanide. Two types of bifunctional activation mode were identified, namely conventional bifunctional Brønsted acid activation and unconventional bifunctional Brønsted–Lewis acid activation. The lowest-energy transition states correspond to the conventional bifunctional mode of activation. The calculated enantiomeric excess, based on eight lowest-energy C–C bond forming transition states, is in good accord with observed enantioselectivity. NCI (noncovalent interaction) analysis of the key transition states reveals extensive noncovalent interactions, including aromatic interactions and hydrogen bonds, between the guanidinium catalyst and substrates. Multiple aryl–aryl interactions between the phenyl groups of guanidine catalyst and the phenyl rings of N-benzhydryl imine are the key stabilizations in the most stable (R)-inducing transition state. Differential attractive aryl–aryl stabilization is the major factor for stereoinduction.

On the possibility to accelerate the thermal isomerizations of overcrowded alkene-based rotary molecular motors with electron-donating or electron-withdrawing substituents

We employ computational methods to investigate the possibility of using electron-donating or electron-withdrawing substituents to reduce the free-energy barriers of the thermal isomerizations that limit the rotational frequencies achievable by synthetic overcrowded alkene-based molecular motors. Choosing as reference systems one of the fastest motors known to date and two variants thereof, we consider six new motors obtained by introducing electron-donating methoxy and dimethylamino or electron-withdrawing nitro and cyano substituents in conjugation with the central olefinic bond connecting the two (stator and rotator) motor halves. Performing density functional theory calculations, we then show that electron-donating (but not electron-withdrawing) groups at the stator are able to reduce the already small barriers of the reference motors by up to 18 kJ mol(-1). This result outlines a possible strategy for improving the rotational frequencies of motors of this kind. Furthermore, exploring the origin of the catalytic effect, it is found that electron-donating groups exert a favorable steric influence on the thermal isomerizations, which is not manifested by electron-withdrawing groups. This finding suggests a new mechanism for controlling the critical steric interactions of these motors. Graphical Abstract The introduction of electron-donating groups in one of the fastest rotary molecular motors known to date is found to reduce the free-energy barriers of the thermal steps that limit the rotational frequencies by up to 18 kJ mol(-1).

The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis

Despite the numerous experimental and theoretical studies on phosphate monoester hydrolysis, significant questions remain concerning the mechanistic details of these biologically critical reactions. In the present work we construct a linear free energy relationship for phosphate monoester hydrolysis to explore the effect of modulating leaving group pK_a on the competition between solvent- and substrate-assisted pathways for the hydrolysis of these compounds. Through detailed comparative electronic-structure studies of methyl phosphate and a series of substituted aryl phosphate monoesters, we demonstrate that the preferred mechanism is dependent on the nature of the leaving group. For good leaving groups, a strong preference is observed for a more dissociative solvent-assisted pathway. However, the energy difference between the two pathways gradually reduces as the leaving group pK_a increases and creates mechanistic ambiguity for reactions involving relatively poor alkoxy leaving groups. Our calculations show that the transition-state structures vary smoothly across the range of pK_as studied and that the pathways remain discrete mechanistic alternatives. Therefore, while not impossible, a biological catalyst would have to surmount a significantly higher activation barrier to facilitate a substrate-assisted pathway than for the solvent-assisted pathway when phosphate is bonded to good leaving groups. For poor leaving groups, this intrinsic preference disappears.

Bifunctional Thioureas with α-Trifluoromethyl or Methyl Groups: Comparison of Catalytic Performance in Michael Additions

Thioureas are an important scaffold in organocatalysis because of their ability to form hydrogen bonds that activate substrates and fix them in a defined position, which allows a given reaction to occur. Structures that enhance the acidity of the thiourea are usually used to increase the hydrogen-bonding properties, such as 3,5-bis(trifluoromethyl)phenyl and boronate ureas. Herein, we report the synthesis of bifunctional thioureas with a chiral moiety that include either a trifluoromethyl or methyl group. Their catalytic performance in representative Michael addition reactions was used in an effort to compare the electronic effects of the fluorination at the methyl group. The observed differences concerning yields and ee values cannot be attributed solely to the different steric environments; theoretical results indicate distinct interactions within the corresponding transition states. The calculated transition states show that the fluorinated catalysts have stronger N-H···O and C-H···F hydrogen bonds, while the nonfluorinated systems have C-H···π contacts. These results have shown that a variety of hydrogen-bonding interactions are important in determining the yield and selectivity of thiourea organocatalysis. These details can be further exploited in catalyst design.

Synergistic Ion-Binding Catalysis Demonstrated via an Enantioselective, Catalytic [2,3]-Wittig Rearrangement

Sigmatropic rearrangements number among the most powerful complexity-building transformations in organic synthesis but have remained largely insensitive to enantioselective catalysis due to the diffuse nature of their transition structures. Here, we describe a synergistic ion-binding strategy for asymmetric catalysis of anionic sigmatropic rearrangements. This approach is demonstrated with the enantioselective [2,3]-Wittig rearrangement of α-allyloxy carbonyl compounds to afford highly enantioenriched homoallylic alcohol products. Chiral thiourea catalysts are shown to engage reactive anions and their countercations through a cooperative set of attractive, noncovalent interactions. Catalyst structure-reactivity-selectivity relationship studies and computational analyses provide insight into catalyst-substrate interactions responsible for enantioinduction and allude to the potential generality of this catalytic strategy.

Theory and Modeling of Asymmetric Catalytic Reactions

Modern density functional theory and powerful contemporary computers have made it possible to explore complex reactions of value in organic synthesis. We describe recent explorations of mechanisms and origins of stereoselectivities with density functional theory calculations. The specific functionals and basis sets that are routinely used in computational studies of stereoselectivities of organic and organometallic reactions in our group are described, followed by our recent studies that uncovered the origins of stereocontrol in reactions catalyzed by (1) vicinal diamines, including cinchona alkaloid-derived primary amines, (2) vicinal amidophosphines, and (3) organo-transition-metal complexes. Two common cyclic models account for the stereoselectivity of aldol reactions of metal enolates (Zimmerman-Traxler) or those catalyzed by the organocatalyst proline (Houk-List). Three other models were derived from computational studies described in this Account. Cinchona alkaloid-derived primary amines and other vicinal diamines are venerable asymmetric organocatalysts. For α-fluorinations and a variety of aldol reactions, vicinal diamines form enamines at one terminal amine and activate electrophilically with NH(+) or NF(+) at the other. We found that the stereocontrolling transition states are cyclic and that their conformational preferences are responsible for the observed stereoselectivity. In fluorinations, the chair seven-membered cyclic transition states is highly favored, just as the Zimmerman-Traxler chair six-membered aldol transition state controls stereoselectivity. In aldol reactions with vicinal diamine catalysts, the crown transition states are favored, both in the prototype and in an experimental example, shown in the graphic. We found that low-energy conformations of cyclic transition states occur and control stereoselectivities in these reactions. Another class of bifunctional organocatalysts, the vicinal amidophosphines, catalyzes the (3 + 2) annulation reaction of allenes with activated olefins. Stereocontrol here is due to an intermolecular hydrogen bond that activates the electrophilic partner in this reaction. We have also studied complex organometallic catalysts. Krische's ruthenium-catalyzed asymmetric hydrohydroxyalkylation of butadiene involves two chiral ligands at Ru, a chiral diphosphine and a chiral phosphate. The size of this combination strains the limits of modern computations with over 160 atoms, multiple significant steps, and a variety of ligand coordinations and conformations possible. We found that carbon-carbon bond formation occurs via a chair Zimmerman-Traxler-type transition structure and that a formyl CH···O hydrogen bond from aldehyde CH to phosphate oxygen, as well as steric interactions of the two chiral ligands, control the stereoselectivity.

Asymmetric tandem hemiaminal-heterocyclization-aza-Mannich reaction of 2-formylbenzonitriles and amines using chiral phase transfer catalysis: an experimental and theoretical study

The first asymmetric synthesis of 3-amino-substituted isoindolinones was accomplished via cascade hemiaminal-heterocyclization-intramolecular aza-Mannich reaction of amines and 2-formylbenzonitriles using chiral phase transfer conditions (PTC).

Importance of the Electron Correlation and Dispersion Corrections in Calculations Involving Enamines, Hemiaminals, and Aminals. Comparison of B3LYP, M06-2X, MP2, and CCSD Results with Experimental Data

While B3LYP, M06-2X, and MP2 calculations predict the ΔG° values for exchange equilibria between enamines and ketones with similar acceptable accuracy, the M06-2X/6-311+G(d,p) and MP2/6-311+G(d,p) methods are required for enamine formation reactions (for example, for enamine 5a, arising from 3-methylbutanal and pyrrolidine). Stronger disagreement was observed when calculated energies of hemiaminals (N,O-acetals) and aminals (N,N-acetals) were compared with experimental equilibrium constants, which are reported here for the first time. Although it is known that the B3LYP method does not provide a good description of the London dispersion forces, while M06-2X and MP2 may overestimate them, it is shown here how large the gaps are and that at least single-point calculations at the CCSD(T)/6-31+G(d) level should be used for these reaction intermediates; CCSD(T)/6-31+G(d) and CCSD(T)/6-311+G(d,p) calculations afford ΔG° values in some cases quite close to MP2/6-311+G(d,p) while in others closer to M06-2X/6-311+G(d,p). The effect of solvents is similarly predicted by the SMD, CPCM, and IEFPCM approaches (with energy differences below 1 kcal/mol).

Experimental and Theoretical Studies in Hydrogen-Bonding Organocatalysis

Chiral thioureas and squaramides are among the most prominent hydrogen-bond bifunctional organocatalysts now extensively used for various transformations, including aldol, Michael, Mannich and Diels-Alder reactions. More importantly, the experimental and computational study of the mode of activation has begun to attract considerable attention. Various experimental, spectroscopic and calculation methods are now frequently used, often as an integrated approach, to establish the reaction mechanism, the mode of activation or explain the stereochemical outcome of the reaction. This article comprises several case studies, sorted according to the method used in their study. The aim of this review is to give the investigators an overview of the methods currently utilized for mechanistic investigations in hydrogen-bonding organocatalysis.

Cross-Aldol Reaction of Isatin with Acetone Catalyzed by Leucinol: A Mechanistic Investigation

Comprehensive mechanistic studies on the enantioselective aldol reaction between isatin (1 a) and acetone, catalyzed by L-leucinol (3 a), unraveled that isatin, apart from being a substrate, also plays an active catalytic role. Conversion of the intermediate oxazolidine 4 into the reactive syn-enamine 6, catalyzed by isatin, was identified as the rate-determining step by both the calculations (ΔG(≠) =26.1 kcal mol(-1) for the analogous L-alaninol, 3 b) and the kinetic isotope effect (kH /kD =2.7 observed for the reaction using [D6 ]acetone). The subsequent reaction of the syn-enamine 6 with isatin produces (S)-2 a (calculated ΔG(≠) =11.6 kcal mol(-1) ). The calculations suggest that the overall stereochemistry is controlled by two key events: 1) the isatin-catalyzed formation of the syn-enamine 6, which is thermodynamically favored over its anti-rotamer 7 by 2.3 kcal mol(-1) ; and 2) the high preference of the syn-enamine 6 to produce (S)-2 a on reaction with isatin (1 a) rather than its enantiomer (ΔΔG(≠) =2.6 kcal mol(-1) ).

A Highly Efficient Chirality Switchable Synthesis of Dihydropyran-Fused Benzofurans by Fine-Tuning the Phenolic Proton of β-Isocupreidine (β-ICD) Catalyst with Methyl

A highly enantioselective β-isocupreidine (β-ICD) catalyzed synthesis of dihydropyran-fused benzofurans through [4+2] cycloaddition of allenoates and benzofuranone alkenes was developed. Switchable chirality inversion of cycloaddition products was achieved by replacing the phenolic proton of the catalyst with a methyl, demonstrating an amazing effect of minimal structural variation on inverting enantioselectivity. DFT calculations were utilized to elucidate the origin of the observed phenomena. Computation also provided a clue for a rational design in which the multi-hydrogen bond with the alcohol additive was found to improve the enantioselectivity of the cycloaddition. Finally, the substrate scope was examined, in which a number of functionalized dihydropyran-fused benzofurans could be obtained in high yields (up to 97 %) with very good regio- (>20:1) and enantioselectivities (up to 98:2 e.r.).

A Friedel-Crafts alkylation mechanism using an aminoindanol-derived thiourea catalyst

Computational calculations based on experimental results shed light on the mechanistic proposal for a Friedel-Crafts alkylation reaction between indole and nitroalkenes, catalysed by a chiral aminoindanol-derived thiourea. In our hypothesis both substrates are simultaneously coordinated to the catalyst in a bifunctional mode. This study elucidates the crucial role played by the hydroxyl group of the catalyst in the success of the reaction. The OH group seems to be involved in the preferential attack of the indole over the nitroalkene, affording the major enantiomer and stabilizing the resulting transition state by a concomitant coordination with the nitroolefin. The results obtained with other catalysts from the same family, and other indoles, are reported and discussed. Theoretical calculations are in agreement with the experimental outcomes and with our previously developed mechanism, displaying the pivotal role played by hydrogen bond interactions.