Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation.

Protein glycation can result in the formation of advanced glycation end products (AGEs), which pose a potential health risk due to their association with diabetic complications. Natural products are a source of drugs discovery and the search for potential natural inhibitors of AGEs is of great significance. Glucosinolates (GSLs) mainly from cruciferous plants have potential antioxidant, anti-inflammatory, and anti-glycation activities. In this study, the inhibitory activity of GSLs on bovine serum albumin (BSA) along with its mechanism was investigated by virtual screening and various computational simulation techniques. Virtual screening revealed that 174 GSLs were screened using Maestro based on the glide score and 89% of the compounds were found to have potential anti-glycation ability with the docking scores less than -5 kcal/mol. Molecular docking showed that the top 10 GSLs were bound to the IIA structural domain of BSA. Among them, glucohesperin (1) and 2-hydroxyethyl glucosinolate (2) had the lowest docking scores of -9.428 and -9.333 kcal/mol, respectively, reflecting their good binding affinity. Molecular dynamics simulations of 1 (ΔG = -43.46 kcal/mol) and 2 (ΔG = -43.71 kcal/mol) revealed that the complexes of these two compounds with proteins had good stability. Further binding site analysis suggested that the mechanism of inhibition of protein glycation by these two active ingredients might be through competitive hydrogen bonding to maintain the structural integrity of the protein, thus inhibiting glycation reaction. Moreover, the ADMET values and CYP450 metabolism prediction data were within the recommended values. Therefore, it can be concluded that 1 and 2 may act as potential anti-glycation agents.

Theoretical studies on 2,3,5,6-Tetra(1H-tetrazol-5-yl)pyrazine and 1,1-diamino-2,2-Dinitroethylene blending system.

To study the properties of 2,3,5,6-tetra(1H-tetrazol-5-yl)pyrazine (H4TTP) and 1,1'-diamino-2,2'-dinitroethylene (FOX-7) blending system, the structures of H4TTP, FOX-7, and H4TTP/FOX-7 dimers were optimized using density functional theory (DFT), and the mechanical properties and cohesive energy densities (CED) of H4TTP/FOX-7 blends with different mass ratios were calculated by molecular dynamics (MD) simulation. The results show that the HOMO of H4TTP is distributed on the pyrazine and tetrazole rings, while the LUMO is mainly distributed on the pyrazine ring, with a small contribution from the tetrazole ring. The HOMO of FOX-7 molecules is mainly located on the CC bonds, while the LUMO is mainly located on the nitro groups. The most stable dimer, (I), was formed when the interaction between frontier MOs is possible and hydrogen bond is formed between two monomers, which was confirmed by the Reduced Density Gradient (RDG) isosurface graph. MD studies were carried out to examine the mechanical properties and cohesive energy density of the blending systems. In monomer systems, FOX-7 has the strongest rigidity and best ductility, while H4TTP has the largest elasticity and best toughness. In the blending systems, we found that various mechanical properties and CED values were different from those of monomers, which improves the sensitivity of H4TTP and the safety of explosives.

Mechanism and Selectivity of Cyclopropanation of 3-Alkenyl-oxindoles with Sulfoxonium Ylides Catalyzed by a Chiral N,N'-Dioxide-Mg(II) Complex.

The mechanism and stereoselectivity of an asymmetric cyclopropanation reaction between 3-alkenyl-oxindole and sulfoxonium ylide catalyzed by a chiral N,N'-dioxide-Mg(II) complex were explored using the B3LYP-D3(BJ) functional and the def2-TZVP basis set. The noncatalytic reaction occurred via a stepwise mechanism, with activation barriers of 21.6-23.5 kcal mol-1. The C2-Cα bond formed followed by the carbanion SN2 substitution, constructing a three-membered ring in spiro-cyclopropyl oxindoles, accompanied by the release of dimethylsulfoxide. The electron-withdrawing N-protecting t-butyloxy carbonyl (Boc) and acetyl (Ac) groups in isatin enhanced the local electrophilicity of the C2 atom and the repulsion between the two COPh groups in the reactants, contributing to high reactivity as well as good diastereoselectivity results. The N-Boc-3-phenacylideneoxindole coordinated to the chiral ligand (L-PiPr2) in a bidentate fashion, forming a hexacoordinate-Mg(II) complex as the reactive species. The origin of enantioselectivity was from the shielding effect of 2,6-diisopropylphenyl groups in the ligand toward the si-face of oxindole. The repulsion between the SO(CH3)2 and COPh groups in 3-alkenyl-oxindole and the neighboring ortho-iPr group in the ligand directed the re-face of ylide to attack the re-face of oxindole preferably, contributing to the high diastereoselectivity of the product. A metal-ion-ligand matching relationship was important for a good asymmetric induction effect of the chiral N,N'-dioxide-metal catalyst. A large chiral cavity in the Zn(II) catalyst weakened the shielding effect of 2,6-diisopropylphenyl groups in the ligand toward the prochiral face of oxindole, leading to inferior enantioselectivity observed in the experiment.

Synthesis, Biological Evaluation, and 3D-QSAR Studies of N-(Substituted pyridine-4-yl)-1-(substituted phenyl)-5-trifluoromethyl-1H-pyrazole-4-carboxamide Derivatives as Potential Succinate Dehydrogenase Inhibitors.

A series of new fungicides that can inhibit the succinate dehydrogenase (SDH) was classified and named as SDH inhibitors by the Fungicide Resistance Action Committee in 2009. To develop more potential SDH inhibitors, we designed and synthesized a novel series of N-(substituted pyridine-4-yl)-1-(substituted phenyl)-5-trifluoromethyl-1H-pyrazole-4-carboxamide derivatives, 4a-4i, namely, 5a-5h, 6a-6h, and 7a-7j. The bioassay results demonstrated that some title compounds exhibited excellent antifungal activity against four tested phytopathogenic fungi (Gibberella zea, Fusarium oxysporum, Cytospora mandshurica, and Phytophthora infestans). The EC50 values were 1.8 µg/mL for 7a against G. zeae, 1.5 and 3.6 µg/mL for 7c against F. oxysporum and C. mandshurica, respectively, and 6.8 µg/mL for 7f against P. infestans. The SDH enzymatic activity testing revealed that the IC50 values of 4c, 5f, 7f, and penthiopyrad were 12.5, 135.3, 6.9, and 223.9 µg/mL, respectively. The molecular docking results of this series of title compounds with SDH model demonstrated that the compounds could completely locate inside of the pocket, the body fragment formed H bonds, and the phenyl ring showed a π-π interaction with Arg59, suggesting that these novel 5-trifluoromethyl-pyrazole-4-carboxamide derivatives might target SDH. These results could provide a benchmark for understanding the antifungal activity against the phytopathogenic fungus P. infestans and prompt us to discover more potent SDH inhibitors.

Author Correction: Structure-antioxidant activity relationship of methoxy, phenolic hydroxyl, and carboxylic acid groups of phenolic acids.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Structure-antioxidant activity relationship of methoxy, phenolic hydroxyl, and carboxylic acid groups of phenolic acids.

The antioxidant activities of 18 typical phenolic acids were investigated using 2, 2'-diphenyl-1-picrylhydrazyl (DPPH) and ferric ion reducing antioxidant power (FRAP) assays. Five thermodynamic parameters involving hydrogen atom transfer (HAT), single-electron transfer followed by proton transfer (SET-PT), and sequential proton-loss electron transfer (SPLET) mechanisms were calculated using density functional theory with the B3LYP/UB3LYP functional and 6-311++G (d, p) basis set and compared in the phenolic acids. Based on the same substituents on the benzene ring, -CH2COOH and -CH = CHCOOH can enhance the antioxidant activities of phenolic acids, compared with -COOH. Methoxyl (-OCH3) and phenolic hydroxyl (-OH) groups can also promote the antioxidant activities of phenolic acids. These results relate to the O-H bond dissociation enthalpy of the phenolic hydroxyl group in phenolic acids and the values of proton affinity and electron transfer enthalpy (ETE) involved in the electron donation ability of functional groups. In addition, we speculated that HAT, SET-PT, and SPLET mechanisms may occur in the DPPH reaction system. Whereas SPLET was the main reaction mechanism in the FRAP system, because, except for 4-hydroxyphenyl acid, the ETE values of the phenolic acids in water were consistent with the experimental results.

A water-stable zinc(ii)-organic framework as a multiresponsive luminescent sensor for toxic heavy metal cations, oxyanions and organochlorine pesticides in aqueous solution.

A novel metal-organic framework with the formula [Zn3(DDB)(DPE)]·H2O (1) (H5DDB = 3,5-di(2',4'-dicarboxylphenyl)benzoic acid and DPE = 1,2-di(4-pyridyl)ethylene) has been solvothermally synthesized by employing a rigid carboxylate ligand H5DDB to assemble with Zn(ii) ions in the presence of a flexible bis(pyridyl) linker DPE. The Zn-MOF is a 3D framework with six-nuclear clusters and possesses remarkable water stability and pH stability. Interestingly, complex 1 can sensitively and selectively sense Fe(iii), Cr(iii), Cr(vi), Mn(vii) and the pesticide 2,6-Dich-4-NA with low detection limits in aqueous solution. Moreover, complex 1 also exhibits selectivity for 2,6-Dich-4-NA detection in real samples including carrot, grape and nectarine extracts, and its detection ability is almost unchanged in the presence of the surfactant sodium dodecyl sulfate (SDS). The possible mechanisms of luminescence quenching have been explained by the weak affinity of nitrogen atoms, resonance energy transfer, and photoinduced electron transfer. To our knowledge, this is the first example of a MOF-based multiresponsive fluorescent probe for the simultaneous detection of Fe(iii), Cr(iii/vi), Mn(vii) and the pesticide 2,6-Dich-4-NA in aqueous solution.

A choline chloride-acrylic acid deep eutectic solvent polymer based on Fe3O4 particles and MoS2 sheets (poly(ChCl-AA DES)@Fe3O4@MoS2) with specific recognition and good antibacterial properties for ß-lactoglobulin in milk.

With the development of deep eutectic solvents (DESs), more DES-based functional materials have been explored and applied in various areas. In this work, a novel choline chloride-acrylic acid (ChCl-AA) DES polymer, on a 2D magnetic base, was prepared for the recognition of ß-lactoglobulin (ß-LG) biomacromolecules in milk and for the inhibition of common bacteria such as Escherichia coli (E. coli), Pseudomonas fluorescens (P. fluorescens), Staphylococcus aureus (S. aureus), and Bacillus subtilis (B. subtilis). The ChCl-AA DESs were polymerized on the surface of 2D MoS2 sheets doped with nano Fe3O4 particles, and the resulting polymer was abbreviated poly(ChCl-AA DES)@Fe3O4@MoS2. The free energy (ΔG=-92) of ChCl-AA DES was calculated using the Gaussian software, the composition and structure of poly(ChCl-AA DES)@Fe3O4@MoS2 were characterized by field emission scanning electron microscopy, transmission electron microscopy, etc., the qualitative and quantitative analyses of ß-LG were done by fluorescence spectra, sodium dodecyl sulfate polyacrylamide gel electrophoresis and high performance liquid chromatography, and the bioactivity of bacteria was analyzed by flat colony counting. Based on the present analysis, poly(ChCl-AA DES)@Fe3O4@MoS2 specifically recognized ß-LG in a good fitting Langmuir isotherm (R2 = 0.9909) and second-order kinetic model (R2 = 0.9989) by affinity, and evidently inhibited three bacteria, namely, E. coil (65%), S. aureus (50%), and B. subtilis (54%), effectively reducing the relative colony number. As the poly(ChCl-AA DES)@Fe3O4@MoS2 material did not only exhibit specific recognition of biomacromolecules, but also had an antimicrobial effect against common bacteria, it could be an ideal separation media or carrier for biomacromolecules in real samples.

Modeling studies on the uptake of hydrogen molecules by graphene.

Detailed ab initio molecular orbital calculations on the interactions of molecular hydrogen, H2, with various poly-aromatic hydrocarbons (PAHs) as a model system for graphene were carried out to accurately describe the physisorption phenomenon. The binding energies corrected for the basis set superposition error, ΔEbind(BSSE), were obtained using the optimized geometries at the MP2 level with a large basis set and were compared with the single point binding energies, denoted as ΔEbind(BSSE-s), using large basis sets on the geometries optimized at the small basis sets, such as SVP and TZVP. The calculations showed that the ΔEbind(BSSE-s) values were similar to those at the MP2 level with the large basis sets. The binding strength increased gradually with increasing size of the PAHs. The ΔEbind(BSSE-s) for an infinite graphene sheet was estimated to be -1.70 kcal mol(-1) using the non-linear curve fitting method. The present work could be expected to provide more useful and reliable information on H2 physisorption.

Trienamine catalysis for asymmetric Diels-Alder reactions of 2,4-dienones: a theoretical investigation.

The mechanism and origin of the selectivity of asymmetric Diels-Alder reactions of 2,4-dienones (R1) by trienamine catalysis is investigated at the M06-2X/6-311++G**(SMD, toluene)//B3LYP/6-311G** level. The acidic additive (salicylic acid or trifluoroacetic acid) promotes the isomerization of the ketoiminium ion into the key reactive cis-trienamine catalytic species with a preferred conformation by constructing a suitable hydrogen-bond bridge for a H shift. One-step cycloaddition was adopted for N-phenylmaleimide (R2), while a stepwise process was used for benzylidenecyanoacetate (R3) dienophile. The -CN and -CO2Et substituents in R3 may play an important role in forming a zwitterionic intermediate by participating in charge transfer by trienamine catalysis. The combination of a hydrogen bond from the protonated N atom of the tertiary amine and steric repulsion from the α-aryl group of trienamine makes the dienophile substrates approach the trienamine from one preferred face. The orbital factors define the most favored alignment of the trienamine and dienophile to realize the endo-selectivity of the product.

Comprehensive studies on the tautomerization of glycine: a theoretical study.

The tautomerization process of glycine between the neutral (NE) and zwitterionic (ZW) forms in aqueous solution was explored theoretically using the conductor-like polarizable continuum model (CPCM) by adopting the PAULING cavity model at the B3LYP, MP2 and CCSD levels with the 6-311+G(d,p) basis set. The tautomerization of glycine is unable to be predicted satisfactorily within the equilibrated framework of the CPCM method. Instead, in this study, three plausible non-equilibrated solvation situations were assumed: (S-1) one water molecule attached to the transferring proton in the ZW moves together with the transferring proton; (S-2) one water molecule attached to the transferring proton in the ZW remains motionless at a fixed position near the NH(2) fragment at the TS structure; and (S-3) proton transfer occurs without changing the position of the surrounding water molecules from their initial state, the ZW form, in the eight water clusters. Although the calculation of (S-3) failed, the Gibbs free energies of activation for tautomerization from the ZW to NE, ΔG(≠)(ZW → NE), was well consistent with the experimental findings in the hypothetical non-equilibrated solvation states of (S-1) and (S-2). This suggests that non-equilibrium solvation is essential to explain the observed experimental data.

Mechanism for the reaction of 2-naphthol with N-methyl-N-phenyl-hydrazine suggested by the density functional theory investigations.

For the first time the computed mechanisms for the novel reaction of 2-naphthol with N-methyl-N-phenylhydrazine, leading to 1-amino-2-naphthol (Tang et al., J Am Chem Soc 2008, 130, 5840), have been investigated using the density functional theory. Four distinct possible pathways were evaluated: two amination mechanisms with the attack of NH(2) group respectively at the α-position C1 and ß-position C3 atoms of 2-naphthol (pathways 1 and 2) as well as two rearrangement processes with displacement of the phenolic hydroxyl group followed by the benzidine-like rearrangement at the α-position C1 and ß-position C3 atoms of 2-naphthol, respectively (pathways 3 and 4). Solvent effect has been tested based on the optimized geometries of the stationary points in solution at the B3LYP/PCM/6-31+G(d,p) level of theory with an averaged dielectric constant of binary solvent. Single-point energies of the optimized structures have been calculated using three hybrid density functionals, B3LYP, MPW3LYP, and B3PW91 with the 6-311++G(3df,2p) basis set. Our computed results clearly manifest that pathway 1 (α-amination) has the highest possibility to occur, with the Gibbs free energies being lower by 6 to 20 kcal/mol compared with the other three pathways, which leads to 1-amino-2-naphthol and N-methylaniline as products. It is in excellent agreement with the experimental observation.

Theoretical investigation on mechanism of asymmetric Michael addition of malononitrile to chalcones catalyzed by Cinchona alkaloid aluminium(III) complex.

The mechanism of Michael addition of malononitrile to chalcones catalyzed by Cinchona alkaloid aluminium(III) complex has been investigated by DFT and ONIOM methods. Calculations indicate that the reaction proceeds through a dual activation mechanism, in which Al(III) acts as a Lewis acid to activate the electrophile α,ß-unsaturated carbonyl substrate while the tertiary amine in the Cinchona alkaloid works as a Lewis base to promote the activation of the malononitrile and deprotonation. A stepwise pathway involving C-C bond formation followed by proton transfer from the catalyst to the carbonyl substrate is adopted, and latter step is predicted to be the rate-determining-step in the reaction with an energy barrier of 12.4 kcal mol(-1). In the absence of the Al(III)-complex, a Cinchona alkaloid activates the carbonyl substrate by a hydrogen bonding of the hydroxyl group, involving a higher energy barrier of 30.4 kcal mol(-1). The steric repulsion between the phenyl group attached to the carbonyl group in the chalcone and isopropoxyl groups of the Al(III)-complex may play an important role in the control of stereoselectivity. The π-π stacking effect between the quinuclidine ring of the quinine and the phenyl group of the chalcones may also help the stabilization of the preferred molecular complex. These results are in agreement with experimental observations.

Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol.

The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.

Reexamination of the π-bond strengths within H2C=XHn systems: a theoretical study.

The accurate determination of π-bond energies, D(π), in doubly-bonded species has been an important issue in theoretical chemistry. The procedure using the divalent state stabilization energy defined by Walsh has been suggested, and the procedure seems to be conceptually reasonable and applicable to all kinds of doubly-bonded species. Therefore, the aim of this study was to examine whether the procedure could be a reliable methodology for estimating the D(π) values for a variety of H(2)C=XH(n) species. To achieve a higher accuracy, the D(π) values were estimated at QCISD(T)/6-311++G(3df,2p) level of theory combined with isogyric correction. The D(π) values estimated in this work were in excellent agreement with the extant literature values. On the other hand, in determining accurate D(π) values for doubly bonded species, especially in species with lone-pair electrons such as H(2)C=O, it has been found that consideration of highly sophisticated electron correlation effects could be important. However, sufficiently accurate D(π) values have been obtainable at QCISD(T) or CCSD(T) levels with a 6-311++G(3df,2p) basis set on geometries at relatively inferior correlated levels such as MP2 and B3LYP levels with a 6-31+G(d) basis set.

Comparative studies on the reactions of acetyl and thioacetyl halides with NH3 in the gas phase and in aqueous solution: a theoretical study.

The reactions of acetyl halides, CH3C(═ O)X and corresponding sulfur analogues, thioacetyl halides, CH3C(=S)X, where X = F and Cl, with NH3 nucleophile were studied theoretically, at the QCISD level of theory, in the gas phase and in aqueous solution. All reactions occurred via the tetrahedral species, and reactions through neutral intermediates both in the gas phase and in aqueous solution could be ruled out, except for the case of the gas-phase reaction of acetyl fluoride. The tetrahedral structure was a transition state (TS) in the reactions of acetyl chloride, while it was a stable intermediate in reactions of thioacetyl halides. These differences could be caused by the π-bond strength of C ═ O and C ═ S. In the case of acetyl fluoride, the T(±)-type species was neither a saddle point nor an energy minimum in the gas phase, but existed as a stable intermediate in aqueous solution due to solvation. Moreover, in reactions of thioacetyl chloride, the rate-limiting step changed from the first step in the gas phase to the second step in aqueous solution, since the zwitterionic intermediates become more stabilized in aqueous solution. However, lower activation energies (ΔG(‡)) in aqueous solution were not caused by the solvent effects, but smaller deformation effects, in going from reactants through the TS.

Barrier effect of dendrons on TiO2 particles in dye sensitized solar cells.

The short circuit current of dye sensitised solar cells increased significantly by the simple addition of polyester hydroxyl acetylene bis(hydroxymethyl)propanoic acid dendrons on TiO(2) nanoparticles, resulting in a very high overall energy conversion efficiency.

Kinetics and mechanism of the anilinolyses of aryl dimethyl, methyl phenyl and diphenyl phosphinates.

The reactions of Z-aryl dimethyl (1), methyl phenyl (2), and diphenyl (3) phosphinates with X-anilines in dimethyl sulfoxide at 60.0 °C are studied kinetically. Kinetic results yield the primary normal deuterium kinetic isotope effects (DKIEs) involving deuterated aniline (XC(6)H(4)ND(2)) nucleophiles, k(H)/k(D) = 1.03-1.17, 1.15-1.29, and 1.24-1.51, and the cross-interaction constants (CICs), ρ(XZ) = 0.37, 0.34, and 0.65 for 1, 2, and 3, respectively. The steric effects of the ligands (R(1) and R(2)) on reaction rates play a role, but are relatively much smaller compared to other phosphinate systems. A stepwise mechanism with a rate-limiting leaving group expulsion from the intermediate is proposed on the basis of the CICs positive signs. The dominant frontside nucleophilic attack through a hydrogen-bonded, four-center-type transition state is proposed on the basis of primary normal DKIEs and large magnitudes of the CICs for 2 and 3, while both frontside and backside attack are proposed on the basis of relatively small primary normal DKIEs for 1.

Theoretical studies on the formation mechanism and explosive performance of nitro-substituted 1,3,5-triazines.

To develop new highly energetic materials, we have considered the design of molecules with high nitrogen content. Possible candidates include 1,3,5-triazine derivatives. In this work, we studied potential synthetic routes for melamine using the MP2/6-31+G(d,p)//B3LYP/6-31G(d) level of theory. The mechanisms studied here are stepwise mechanism beginning with the dimerization of cyanamide and one-step termolecular mechanism. The same type of mechanism is also applied to nitro-substituted 1,3,5-triazines. Values for the heat of formation in the solid phase were predicted from density functional theory calculations. Densities were estimated from a regression equation obtained by molecular surface electrostatic potentials. The Cheetah program was used to study the explosive performance of these compounds. In this study, we found that the explosive properties of 2-amino-4, 6-dinitro-1, 3,5-triazine (ADNTA), and 2,4,6-trinitro-1,3,5-triazine (TNTA) are similar to those of RDX and HMX, respectively.

Mechanisms of norbornadiene dimerization to Binor-S using cationic Co(I), Rh(I), and Ir(I) catalysts.

We investigated the transition metal-catalyzed reaction mechanisms of NBD dimerization to Binor-S using cationic Co(I), Rh(I), and Ir(I) catalysts, using mPW1PW91, mPW1K, and B3LYP density functional methods. Our results indicate that the monomeric metal center has the ability to bind with four double bonds of two NBD molecules with a syn spatial geometry to form a penta-coordinated complex. We designed three possible pathways, but found two of them blocked. The favored pathway involves three steps from the reactant precursor to the product precursor: the first step is the formation of a single bond to connect two NBD units, the second is the alkene insertion leading to the formation of the three-membered ring structure, and the final step is the formation of the final product precursor. Orbital analysis showed metal...C-C sigma agostic interaction in the product precursor, which is in agreement with the previous experimental findings. In addition, we found that the solvent and counter-ions had significant effects on the dimerization reactions.