CircAGFG1 absence decreases PKM2 expression to enhance oxaliplatin sensitivity in colorectal cancer in a miR-7-5p-dependent manner.

Circular RNA (circRNA) ArfGAP with FG repeats 1 (circAGFG1) contributes to colorectal cancer (CRC) development. However, whether circAGFG1 regulates the resistance of CRC to oxaliplatin (L-OHP) remains unknown. CircAGFG1, microRNA-7-5p (miR-7-5p) and pyruvate kinase M2 (PKM2) RNA expression were quantified by quantitative real-time polymerase chain reaction. Protein expression was detected by western blot assay and immunohistochemistry assay. Glycolysis was analyzed through glucose uptake, lactate production and adenosine triphosphate (ATP) concentration assays. 50% inhibitory concentration of L-OHP was determined by cell counting kit-8 assay. Cell proliferation and apoptotic rate were analyzed by cell colony formation and flow cytometry analysis, respectively. Dual-luciferase reporter assay was used to identify the relationship among circAGFG1, miR-7- 5p and PKM2. The effect of circAGFG1 on L-OHP sensitivity in vivo was further evaluated by a xenograft model assay. CircAGFG1 and PKM2 expression were significantly increased, while miR-7-5p was decreased in L-OHP-resistant CRC tissues and cells. High circAGFG1 expression predicted a poor prognosis of CRC. CircAGFG1 knockdown or PKM2 depletion decreased glycolysis and cell proliferation and increased L-OHP sensitivity and cell apoptosis. PKM2 introduction rescued circAGFG1 silencing-induced effects in CRC cells. In terms of mechanism, circAGFG1 bound to miR-7-5p, which was identified to target PKM2. Also, circAGFG1 regulated PKM2 expression by interacting with miR-7-5p. Further, circAGFG1 knockdown improved the sensitivity of tumors to L-OHP in vivo. CircAGFG1 depletion inhibited L-OHP resistance by regulating the miR-7-5p/PKM2 pathway.

Fast heritability estimation based on MINQUE and batch training.

Heritability, the proportion of phenotypic variance explained by genome-wide single nucleotide polymorphisms (SNPs) in unrelated individuals, is an important measure of the genetic contribution to human diseases and plays a critical role in studying the genetic architecture of human diseases. Linear mixed model (LMM) has been widely used for SNP heritability estimation, where variance component parameters are commonly estimated by using a restricted maximum likelihood (REML) method. REML is an iterative optimization algorithm, which is computationally intensive when applied to large-scale datasets (e.g. UK Biobank). To facilitate the heritability analysis of large-scale genetic datasets, we develop a fast approach, minimum norm quadratic unbiased estimator (MINQUE) with batch training, to estimate variance components from LMM (LMM.MNQ.BCH). In LMM.MNQ.BCH, the parameters are estimated by MINQUE, which has a closed-form solution for fast computation and has no convergence issue. Batch training has also been adopted in LMM.MNQ.BCH to accelerate the computation for large-scale genetic datasets. Through simulations and real data analysis, we demonstrate that LMM.MNQ.BCH is much faster than two existing approaches, GCTA and BOLT-REML.

A review of SNP heritability estimation methods.

Over the past decade, statistical methods have been developed to estimate single nucleotide polymorphism (SNP) heritability, which measures the proportion of phenotypic variance explained by all measured SNPs in the data. Estimates of SNP heritability measure the degree to which the available genetic variants influence phenotypes and improve our understanding of the genetic architecture of complex phenotypes. In this article, we review the recently developed and commonly used SNP heritability estimation methods for continuous and binary phenotypes from the perspective of model assumptions and parameter optimization. We primarily focus on their capacity to handle multiple phenotypes and longitudinal measurements, their ability for SNP heritability partition and their use of individual-level data versus summary statistics. State-of-the-art statistical methods that are scalable to the UK Biobank dataset are also elucidated in detail.

Insights into the N-Heterocyclic Carbene (NHC)-Catalyzed Oxidative γ-C(sp3)-H Deprotonation of Alkylenals and Cascade [4 + 2] Cycloaddition with Alkenylisoxazoles.

The N-heterocyclic carbene (NHC)-catalyzed oxidative C-H deprotonations have attracted increasing attention; however, the general mechanism regarding this kind of oxidative organocatalysis remains unclear. In this paper, the competing mechanisms and origin of the stereoselectivity of the NHC-catalyzed oxidative γ-C(sp3)-H deprotonation of alkylenals and cascade [4 + 2] cycloaddition with alkenylisoxazoles were systematically investigated for the first time using density functional theory (DFT). The computed results indicate that the oxidation of the Breslow intermediate by 3,3',5,5'-tetra- tert-butyl diphenoquinone (DQ) via a hydride transfer to oxygen (HTO) pathway is the most favorable among the four competing pathways. In addition, the analyses demonstrate that oxidant DQ plays a double role, i.e., strengthening the acidity of the hydrogen of the γ-carbon of alkylenal and forming π···π interactions with conjugated C═C bonds to promote the γ-C(sp3)-H deprotonation. The NHC catalyst acts as a Lewis base, and the hydrogen-bond network between the NHC and the substrate formed in the key Michael addition step is responsible for the origin of the stereoselectivity. Further DFT calculations reveal that the nonpolar solvent can stabilize the nonpolar R isomer but destabilize the polar S isomer for the stereoselectivity-determining transition states, thus improving the stereoselectivity.

Insights into the N-Heterocyclic Carbene (NHC)-Catalyzed Intramolecular Cyclization of Aldimines: General Mechanism and Role of Catalyst.

One of the most challenging questions in the Lewis base organocatalyst field is how to predict the most electrophilic carbon for the complexation of N-heterocyclic carbene (NHC) and reactant. This study provides a valuable case for this issue. Multiple mechanisms (A, B, C, D, and E) for the intramolecular cyclization of aldimine catalyzed by NHC were investigated by using density functional theory (DFT). The computed results reveal that the NHC energetically prefers attacking the iminyl carbon (AIC mode, which is associated with mechanisms A and C) rather than attacking the olefin carbon (AOC mode, which is associated with mechanisms B and D) or attacking the carbonyl carbon (ACC mode, which is associated with mechanism E) of aldimine. The calculated results based on the different reaction models indicate that mechanism A (AIC mode), which is associated with the formation of the aza-Breslow intermediate, is the most favorable pathway. For mechanism A, there are five steps: (1) nucleophilic addition of NHC to the iminyl carbon of aldimine; (2) [1,2]-proton transfer to form an aza-Breslow intermediate; (3) intramolecular cyclization; (4) the other [1,2]-proton transfer; and (5) regeneration of NHC. The analyses of reactivity indexes have been applied to explain the chemoselectivity, and the general principles regarding the possible mechanisms would be useful for the rational design of NHC-catalyzed chemoselective reactions.

Computational Study on γ-C-H Functionalization of α,ß-Unsaturated Ester Catalyzed by N-Heterocyclic Carbene: Mechanisms, Origin of Stereoselectivity, and Role of Catalyst.

The N-heterocyclic carbene (NHC)-catalyzed γ-C-H deprotonation/functionalization of α,ß-unsaturated esters with hydrazones leading to the δ-lactams has been theoretically investigated by using density functional theory. Three possible reaction mechanisms including Mechanism A, for which the NHC catalyst serves as a nucleophilic catalyst to attack on the carbonyl carbon atom to initiate the reaction, Mechanism B, in which NHC triggers the reaction through the hydrogen bond, and Mechanism C, which is the direct deprotonation/functionalization process without the presence of NHC, have been suggested and studied in detail. The most favorable Mechanism A was identified to proceed through the following processes: nucleophilic attack on the carbonyl carbon of the ester by NHC, γ-deprotonation, formal [4 + 2] cycloaddition of dienolate with hydrazone, and regeneration of NHC. Multiple possible deprotonation pathways were explored, and the additive base such as K2CO3 would significantly lower the energy barrier. The formal [4 + 2] cycloaddition step is the stereoselectivity-determining step, and R-configured rather than S-configured product was preferentially generated. In addition, the C-H···O, C-H···N, LP···π, and C-H···π interactions have been identified in the most energetically favorable transition state involved in the stereoselectivity-determining step. The additional analysis indicates that NHC strengthens the acidity and electrophilicity to promote the deprotonation, indicating this is not a simple NHC-catalyzed umpolung carbonyl reaction. The mechanistic insights and the significant role of NHC obtained in this study should provide valuable insights for understanding the organocatalytic γ-C(sp3)-H bond functionalization reaction.

Density functional theory study on structure and stability of BeBn+ clusters.

RATIONALE: Boride compounds hold promise for broad applications in the field of optoelectronics due to their high-temperature resistant, corrosion resistant and antioxidant properties. In order to reveal the formation mechanism of alkali and alkaline earth metal doped boron clusters, theoretical studies of these systems are required. METHODS: All the possible geometrical structures of BeBn+ clusters (n = 1-8) were optimized at the B3LYP/6-311+G(d) level; the harmonic vibration frequencies were obtained to examine the true stability and give the zero-point vibration energy at that theoretical level. The single point energies of all the structures were computed at the CCSD(T)/aug-cc-pVDZ level. For the most stable structures, the average binding energy (Eb ), the fragmentation energy (EF ) and second-order difference of total energy (Δ2 E) were used to evaluate the relative stability of clusters. RESULTS: Most of the BeBn+ clusters are planar in structure; the B atoms tend to aggregate to form a boron ring, and the coordinating Be atoms are on the periphery of the clusters. The fragmentation energy and second-order difference of total energy show that there is an obvious odd-even alteration as n increases, and local-maxima when n is odd. CONCLUSIONS: A systematic theoretical investigation on the geometries, stabilities and electronic properties of BeBn+ clusters has been carried out where n = 1-8. The results provide a useful reference for understanding the formation mechanism and stability of these clusters, as well as guidance for finding larger size clusters.

Water sandwiched by a pair of aromatic rings in a proton-conducting metal-organic framework.

The interactions between water molecules and aromatic rings are known to be common and important in physics, chemistry and life sciences. Benzene-water complexes are the main prototype systems for O-Hπ and lone-pair (lp)π interactions in theoretical research, however solid state examples are very rare. Here, the solid state example of water sandwiched by a pair of aromatic rings is observed in a silver-mellitate framework, where lpπ and O-Hπ interactions coexist. The coexistence of these two interactions has been further verified by theoretical calculations. In addition, ammonium ions and water molecules as proton sources, and strongly H-bonded nets as the pathway of proton transport, make the reported MOFs (metal-organic frameworks) exhibit distinct proton conduction.

A computational study on the N-heterocyclic carbene-catalyzed Csp(2)-Csp(3) bond activation/[4+2] cycloaddition cascade reaction of cyclobutenones with imines: a new application of the conservation principle of molecular orbital symmetry.

A comprehensive density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the Csp(2)-Csp(3) single bond activation of cyclobutenones and their [4+2] cycloaddition reaction with imines via N-heterocyclic carbene (NHC) organocatalysis. According to our calculated results, the fundamental reaction pathway contains four steps: nucleophilic addition of NHC to cyclobutenone, C-C bond cleavage for the formation of an enolate intermediate, [4+2] cycloaddition of the enolate intermediate with isatin imine, and the elimination of the NHC catalyst. In addition, the calculated results also reveal that the second reaction step is the rate-determining step, whereas the third step is the regio- and stereo-selectivity determining step. For the regio- and stereo-selectivity determining step, all four possible attack modes were considered. The addition of the C[double bond, length as m-dash]N bond in isatin imine to the dienolate intermediate is more energy favorable than the addition of the C[double bond, length as m-dash]O bond to a dienolate intermediate. Moreover, the Re face addition of the C[double bond, length as m-dash]N bond in isatin imine to the Re face of the dienolate intermediate leading to the SS configuration N-containing product was demonstrated to be most energy favorable, which is mainly due to the stronger second-order perturbation energy value in the corresponding transition state. Furthermore, by tracking the frontier molecular orbital (FMO) changes in the rate-determining C-C bond cleavage step, we found that the reaction obeys the conservation principle of molecular orbital symmetry. We believe that the present work would provide valuable insights into this kind of reaction.

Insights into Stereoselective Aminomethylation Reaction of α,ß-Unsaturated Aldehyde with N,O-Acetal via N-Heterocyclic Carbene and Brønsted Acid/Base Cooperative Organocatalysis.

A theoretical investigation has been performed to interrogate the mechanism and stereoselectivities of aminomethylation reaction of α,ß-unsaturated aldehyde with N,O-acetal, which is initiated by N-heterocyclic carbene and Brønsted acid (BA). The calculated results disclose that the reaction contains several steps, i.e., formation of the actual catalysts NHC and Brønsted acid Et3N·H(+) coupled with activation of C-O bond of N,O-acetal, nucleophilic attack of NHC on α,ß-unsaturated aldehyde, formation of Breslow intermediate, ß-protonation for the formation of enolate intermediate, nucleophilic addition on the Re/Si face to enolate by the activated iminium cation, esterification coupled with regeneration of Et3N·H(+), and dissociation of NHC from product. Addition on the prochiral face of enolate should be the stereocontrolling step, in which the chiral α-carbon is formed. Furthermore, NBO, GRI, and FMO analyses have been performed to explore the roles of catalysts and origin of stereoselectivity. Surprisingly, the added Brønsted base (BB) Et3N plays an indispensable role in the esterification process, indicating the reaction proceeds under NHC-BA/BB multicatalysis rather than NHC-BA dual catalysis proposed in the experiment. This theoretical work provides a case on the exploration of the special roles of the multicatalysts in NHC chemistry, which is valuable for rational design on new cooperative organocatalysis.

A DFT study on NHC-catalyzed intramolecular aldehyde-ketone crossed-benzoin reaction: mechanism, regioselectivity, stereoselectivity, and role of NHC.

A systematic theoretical study has been carried out to understand the mechanism and stereoselectivity of N-heterocyclic carbene (NHC)-catalyzed intramolecular crossed-benzoin reaction of enolizable keto-aldehyde using density functional theory (DFT) calculations. The calculated results reveal that the most favorable pathway contains four steps, i.e., the nucleophilic attack of NHC on the carbonyl carbon atom of a formyl group, the formation of a Breslow intermediate, a ring-closure process coupled with proton transfer, and regeneration of the catalyst. For the formation of the Breslow intermediate via the [1,2]-proton transfer process, apart from the direct proton transfer mechanism, the base Et3N and the in situ generated Brønsted acid Et3N·H(+) mediated proton transfer mechanisms have also been investigated; the free energy barriers for the crucial proton transfer steps are found to be significantly lowered by explicit inclusion of the Brønsted acid Et3N·H(+). The computational results show that the ring-closure process is the stereoselectivity-determining step, in which two chirality centers assigned on the coupling carbon atoms are formed, and the S-configured diastereomer is the predominant product, which is in good agreement with the experimental observations. NCI and NBO analyses are employed to disclose the origin of stereoselectivity and regioselectivity. Moreover, a global reaction index (GRI) analysis has been performed to confirm that NHC mainly plays the role of a Lewis base. The mechanistic insights obtained in the present study should be valuable for the rational design of an effective organocatalyst for this kind of reaction with high stereoselectivity and regioselectivity.

Energetics and kinetics of Cu atoms and clusters on the Si(111)-7 × 7 surface: first-principles calculations.

Exploring the properties of noble metal atoms and nano- or subnano-clusters on the semiconductor surface is of great importance in many surface catalytic reactions, self-assembly processes, crystal growth, and thin film epitaxy. Here, the energetics and kinetic properties of a single Cu atom and previously reported Cu magic clusters on the Si(111)-(7 × 7) surface are re-examined by the state-of-the-art first-principles calculations based on density functional theory. First of all, the diffusion path and high diffusion rate of a Cu atom on the Si(111)-(7 × 7) surface are identified by mapping out the total potential energy surface of the Cu atom as a function of its positions on the surface, supporting previous experimental hypothesis that the apparent triangular light spots observed by scanning tunneling microscopy (STM) are resulted from a single Cu atom frequently hopping among adjacent adsorption sites. Furthermore, our findings confirm that in the low coverage of 0.15 monolayer (ML) the previously proposed hexagonal ring-like Cu6 cluster configuration assigned to the STM pattern is considerably unstable. Importantly, the most stable Cu6/Si(111) complex also possesses a distinct simulated STM pattern with the experimentally observed ones. Instead, an energetically preferred solid-centered Cu7 structure exhibits a reasonable agreement between the simulated STM patterns and the experimental images. Therefore, the present findings convincingly rule out the tentative six-atom model and provide new insights into the understanding of the well-defined Cu nanocluster arrays on the Si(111)-(7 × 7) surface.

A DFT study on PBu3-catalyzed intramolecular cyclizations of N-allylic substituted α-amino nitriles for the formation of functionalized pyrrolidines: mechanisms, selectivities, and the role of catalysts.

The mechanisms and chemo- and stereo-selectivities of PBu3-catalyzed intramolecular cyclizations of N-allylic substituted α-amino nitriles leading to functionalized pyrrolidines (5-endo-trig cyclization, Mechanism A) and their competing reaction leading to another kind of pyrrolidine (5-exo-trig cyclization, Mechanism B) have been investigated using density functional theory (DFT). Multiple possible reaction pathways associated with four different isomers (RR, SR, RS, and SS) for Mechanism A, and two isomers (R and S) for Mechanism B have been studied. The calculated results indicate that the Gibbs free energy barriers of Mechanism A are remarkably lower than those of Mechanism B, and the reaction pathway leading to the RS-configured product has the lowest Gibbs free energy barrier, which is in agreement with the experiments. A C-H···π interaction has been identified to be responsible for the favorability of RS isomers by non-covalent interaction (NCI) analysis. Moreover, global reaction indexes (GRIs) and NBO analyses confirm that PBu3 acts as a Lewis base to strengthen the nucleophilicity of the reaction active site. The mechanistic insights gained in the present study should be valuable for the rational design of effective organocatalysts for this kind of reaction with high chemo- and stereo-selectivities.

Theoretical studies on binding modes of copper-based nucleases with DNA.

In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by "gap DNA". The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.

DFT Study on the Mechanism and Stereoselectivity of NHC-Catalyzed Synthesis of Substituted Trifluoromethyl Dihydropyranones with Contiguous Stereocenters.

Recently, Smith and co-workers reported an interesting work that provides a facile approach to access substituted trifluoromethyl dihydropyranones with two contiguous stereocenters by utilizing the α,ß-unsaturated trifluoromethyl ketones as a substrate for NHC-catalyzed [4 + 2] cycloadditions. The most significant point of this reaction lies in the capability of introducing substituents to the C(5) position of the dihydropyranones. In the present study, we performed detailed DFT investigations toward the catalytic mechanism of this reaction, and determined origins of the diastereo- and enatioselectivities through analyses on distortion energies of two key stationary species and on components of Gibbs free energy barriers of elementary steps in which the stereocenters are generated. The theoretically predicted configuration of the main product was well-consistent with the experimental results, and the excellent correlation between the relative free energy barriers (ΔΔG(298)(0)) with the relative enthalpy barriers (ΔΔH(298)(0)) indicates that the stereoselectivity should originate from differences of enthalpy barriers rather than distinctions of the entropy item (-TΔS(298)(0)) changes. The systematic study of the substituent effect affords conclusive evidence for the catalytic mechanism we proposed but failed to give any clue to how the various electronic properties of substituents act on the experimental yields.

A Lightweight Social Computing Approach to Emergency Management Policy Selection.

In order to select effective policies for emergency management in a timely manner, this paper proposes an agile and lightweight social computing approach to facilitating policy selection, evaluation, and adjustment relative to emergency management in both quantitative and qualitative ways. The approach consists of three components represented as PZE: 1) (P) emergency management policy selecting; 2) (Z) modeling artificial societies with the zombie-city model (a general and formal artificial society model); and 3) (E) policy evaluation. The formal specification of the zombie-city model and rigorous expressions of scenarios enable rigorous description and formal reasoning of an artificial society. A feedback loop of this approach supports the iterative adjustment of emergency management policies and the creation of more effective policies. This approach is verified by applying it to a case of an infectious disease transmission with quantitative evaluations, qualitative reasoning and analysis, and iterative adjustments. Results indicate effective emergency management policies can be established with the approach in an iterative way. In contrast with existing research, our proposed approach offers the benefits of being simple, general, rapidly adaptive to changes, and low cost.

Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn-Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?

Coupled-cluster (CC) methods have been extensively used as the high-level approach in quantum electronic structure theory to predict various properties of molecules when experimental results are unavailable. It is often assumed that CC methods, if they include at least up to connected-triple-excitation quasiperturbative corrections to a full treatment of single and double excitations (in particular, CCSD(T)), and a very large basis set, are more accurate than Kohn-Sham (KS) density functional theory (DFT). In the present work, we tested and compared the performance of standard CC and KS methods on bond energy calculations of 20 3d transition metal-containing diatomic molecules against the most reliable experimental data available, as collected in a database called 3dMLBE20. It is found that, although the CCSD(T) and higher levels CC methods have mean unsigned deviations from experiment that are smaller than most exchange-correlation functionals for metal-ligand bond energies of transition metals, the improvement is less than one standard deviation of the mean unsigned deviation. Furthermore, on average, almost half of the 42 exchange-correlation functionals that we tested are closer to experiment than CCSD(T) with the same extended basis set for the same molecule. The results show that, when both relativistic and core-valence correlation effects are considered, even the very high-level (expensive) CC method with single, double, triple, and perturbative quadruple cluster operators, namely, CCSDT(2)Q, averaged over 20 bond energies, gives a mean unsigned deviation (MUD(20) = 4.7 kcal/mol when one correlates only valence, 3p, and 3s electrons of transition metals and only valence electrons of ligands, or 4.6 kcal/mol when one correlates all core electrons except for 1s shells of transition metals, S, and Cl); and that is similar to some good xc functionals (e.g., B97-1 (MUD(20) = 4.5 kcal/mol) and PW6B95 (MUD(20) = 4.9 kcal/mol)) when the same basis set is used. We found that, for both coupled cluster calculations and KS calculations, the T1 diagnostics correlate the errors better than either the M diagnostics or the B1 DFT-based diagnostics. The potential use of practical standard CC methods as a benchmark theory is further confounded by the finding that CC and DFT methods usually have different signs of the error. We conclude that the available experimental data do not provide a justification for using conventional single-reference CC theory calculations to validate or test xc functionals for systems involving 3d transition metals.

Theoretical Investigations toward the Asymmetric Insertion Reaction of Diazoester with Aldehyde Catalyzed by N-Protonated Chiral Oxazaborolidine: Mechanisms and Stereoselectivity.

In recent years, the N-protonated chiral oxazaborolidine has been utilized as the Lewis acid catalyst for the asymmetric insertion reaction, which is one of the most challenging topics in current organic chemistry. Nevertheless, the reaction mechanism, stereoselectivity, and regioselectivity of this novel insertion reaction are still unsettled to date. In this present work, the density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the formal C-C/H insertion reaction between benzaldehyde and methyl α-benzyl diazoester catalyzed by the N-protonated chiral oxazaborolidine. For the reaction channel to produce the R-configured C-C insertion product as the predominant isomer, the catalytic cycle can be characterized by four steps: (i) the complexation of the aldehyde with catalyst, (ii) addition of the other reactant methyl α-benzyl diazoester, (iii) the removal of nitrogen concerted with the migration of phenyl group or hydrogen, and (iv) the dissociation of catalyst from the products. Our computational results show that the carbon-carbon bond formation step is the stereoselectivity determining step, and the reaction pathways associated with [1, 2]-phenyl group migration occur preferentially to those pathways associated with [1, 2]-hydrogen migration. The pathway leading to the R-configured product is the most favorable pathway among the possible stereoselective pathways. All these calculated outcomes align well with the experimental observations. The novel mechanistic insights should be valuable for understanding this kind of reaction.

Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA).

In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is a nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-O(γ) atom. The last step is a proton transfer from Thr1-N(z) to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal mol(-1), which is reasonably close to the activation free energy (∼22.4-23.0 kcal mol(-1)) derived from the available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved in a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at a molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome.

Mechanisms and stereoselectivities of the Rh(I)-catalyzed carbenoid carbon insertion reaction of benzocyclobutenol with diazoester.

In this study, a density functional theory (DFT) study has been carried out to investigate the mechanisms of Rh(I)-catalyzed carbenoid carbon insertion into a C-C bond reaction between benzocyclobutenol (R1) and diazoester (R2). The calculated results indicate that the reaction proceeds through five stages: deprotonation of R1, cleavage of the C-C bond, carbenoid carbon insertion, intramolecular aldol reaction, and protonation of the alkoxyl-Rh(I) intermediate. We have suggested and studied two possible pathways according to different coordination patterns (including ketone-type and enol-type coordination forms) in the fourth stage and found that the enol-type pathway is favorable, making the coordination mode of the Rh(I) center in the oxa-π-allyl Rh(I) intermediate clear in this reaction system. Moreover, four possible protonation channels have been calculated in the fifth stage, and the computational results show that the H2O-assisted proton transfer channel is the most favorable. The first step of the third stage is rate-determining, and the first steps in stages 3 and 4 play important roles in determining the stereoselectivities. Moreover, the analyses of distortion/interaction, natural bond orbital (NBO), and molecular orbital (MO) have been performed to better understand this title reaction. Furthermore, the pathway corresponding to the RR configurational product is the most favorable path, which is consistent with the experimental result. This work should be helpful for understanding the detailed reaction mechanism and the origin of stereoselectivities of the title reaction and thus could provide valuable insights into rational design of more efficient catalysts for this type of reactions.