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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

New mechanistic insight into stepwise metal-center exchange in a metal-organic framework based on asymmetric Zn(4) clusters.

Herein, a mechanism of stepwise metal-center exchange for a specific metal-organic framework, namely, [Zn4 (dcpp)2 (DMF)3 (H2 O)2 ]n (H4 dcpp=4,5-bis(4'-carboxylphenyl)phthalic acid), is disclosed for the first time. The coordination stabilities between the central metal atoms and the ligands as well as the coordination geometry are considered to be dominant factors in this stepwise exchange mechanism. A new magnetic analytical method and a theoretical model confirmed that the exchange mechanism is reasonable. When the metathesis reaction occurs between Cu(II) ions and framework Zn(II) ions, the magnetic exchange interaction of each pair of Cu(II) centers gradually strengthens with increasing amount of framework Cu(II) ions. By analyzing the changes of coupling constants in the Cu-exchanged products, it was deduced that Zn4 and Zn3 are initially replaced, and then Zn1 and Zn2 are replaced later. The theoretical calculation further verified that Zn4 is replaced first, Zn3 next, then Zn1 and Zn2 last, and the coordination stability dominates the Cu/Zn exchange process. For the Ni/Zn and Co/Zn exchange processes, besides the coordination stability, the preferred coordination geometry was also considered in the stepwise-exchange behavior. As Ni(II) and Co(II) ions especially favor octahedral coordination geometry in oxygen-ligand fields, Ni(II) ions and Co(II) ions could only selectively exchange with the octahedral Zn(II) ions, as was also confirmed by the experimental results. The stepwise metal-exchange process occurs in a single crystal-to-single crystal fashion.

Highly enantioselective catalytic system for asymmetric copolymerization of carbon dioxide and cyclohexene oxide.

A new ligand can be easily prepared, and its intramolecular dinuclear zinc complexes act as a high performance catalyst for the asymmetric alternating copolymerization of cyclohexene oxide and CO2 under very mild conditions (1 atm CO2 , room temperature), affording completely alternating polycarbonates with up to 93.8 % enantiomeric excess (ee) and 98 % yield. A high Mn value of 28 600 and a relatively narrow polydispersity (Mw /Mn ratio) of 1.43 were also achieved.

DFT study on the mechanisms and stereoselectivities of the [4 + 2] cycloadditions of enals and chalcones catalyzed by N-heterocyclic carbene.

The possible reaction mechanisms of stereoselective [4 + 2] cycloaddition of enals and chalcones catalyzed by N-heterocyclic carbene (NHC) have been investigated using density functional theory (DFT). The calculated results indicate that the most favorable reaction channel occurs through five steps. The first step is the nucleophilic attack on the enal by NHC. Then, there are two consecutive acid (AcOH)-assisted proton-transfer steps. Subsequently, the fourth step is the [4 + 2] cycloaddition process associated with the formation of two chiral centers, followed by dissociation of NHC and product. Our computational results demonstrate that the [4 + 2] cycloaddition is the rate-determining and stereoselectivity-determining step. The energy barrier for the SS configurational channel (17.62 kcal/mol) is the lowest one, indicating the SS configurational product should be the main product, which is in agreement with experiment. Moreover, the role of NHC catalyst in the [4 + 2] cycloaddition of enal and chalcone was explored by the analysis of global reactivity indexes. This work should be helpful for realizing the significant roles of catalyst NHC and the additive AcOH and thus provide valuable insights on the rational design of potential catalyst for this kind of reactions.

A highly sensitive C3-symmetric Schiff-base fluorescent probe for Cd2+.

A new C3-symmetric Schiff-base fluorescent probe (L) based on 8-hydroxy-2-methylquinoline has been developed. As expected, the probe L can display high fluorescent selectivity for Cd(2+) over Zn(2+) and most other common ions in neutral ethanol aqueous medium. Moreover, the mechanism of the L-Cd(2+) complex has been confirmed by X-ray crystallography and density functional theory calculation results. More importantly, L could be used to image Cd(2+) within living cells.

DFT study on the reaction mechanisms and stereoselectivities of NHC-catalyzed [2 + 2] cycloaddition between arylalkylketenes and electron-deficient benzaldehydes.

In this paper, two possible mechanisms (mechanisms A and B) on the stereoselective [2 + 2] cycloaddition of aryl(alkyl)ketenes and electron-deficient benzaldehydes catalyzed by N-heterocyclic carbenes (NHCs) have been investigated using density functional theory (DFT). Our calculated results indicate that the favorable mechanism (mechanism A) includes three processes: the first step is the nucleophilic attack on the arylalkylketene by the NHC catalyst to form an intermediate, the second step is the [2 + 2] cycloaddition of the intermediate and benzaldehyde for the formation of a ß-lactone, and the last step is the dissociation of the NHC catalyst and the ß-lactone. Notably, the [2 + 2] cycloaddition, in which two chiral centers associated with four configurations (SS, RR, SR and RS) are formed, is demonstrated to be both the rate- and stereoselectivity-determining step. Moreover, the reaction pathway associated with the SR configuration is the most favorable pathway and leads to the main product, which is in good agreement with the experimental results. Furthermore, the analysis of global and local reactivity indexes has been performed to explain the role of the NHC catalyst in the [2 + 2] cycloaddition reaction. Therefore, this study will be of great use for the rational design of more efficient catalysts for this kind of cycloaddition.

A theoretical study on the mechanisms of the reactions between 1,3-dialkynes and ammonia derivatives for the formation of five-membered N-heterocycles.

The reactions between 1,3-dialkynes and ammonia derivatives (such as hydrazine and hydroxylamine) for the formation of five-membered N-heterocycles (i.e. 3,5-disubstituted pyrazole and 3,5-disubstituted isoxazole) have been investigated using the density functional theory (DFT) method. The calculated results indicate that the favorable mechanism of this kind of reaction generally contains four processes: (1) the Cope-type hydroamination reaction between the reactants coupled with the hydrazine/hydroxylamine-assisted proton transfer process or the trimolecular hydroamination reaction via a six-membered transition state, (2) the bimolecular proton transfer process for the formation of an allenyl oxime intermediate, (3) the cyclization process, and (4) another bimolecular or hydrazine/hydroxylamine-assisted proton transfer process to afford the final products (3,5-disubstituted pyrazole and 3,5-disubstituted isoxazole). The computational results demonstrate that the novel bimolecular proton transfer process occurs in a stepwise manner and the first step of the novel bimolecular proton transfer process is calculated to be the rate-determining step in both the reactions, and their energy barriers are 28.45 kcal mol(-1) associated with the formation of 3,5-disubstituted pyrazole and 31.07 kcal mol(-1) associated with the formation of 3,5-disubstituted isoxazole. In particular, the novel bimolecular proton transfer process has reasonably explained in detail on how and why this kind of reaction occurs, and this would provide valuable clues for the rational design of Brønsted acid/base catalysts to promote the synthesis of the five-membered N-heterocyclic compounds.