W. M. C. Sameera

The artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy is an automatic approach to explore all important reaction paths of complex reactions. Most traditional methods in computational catalysis require guess reaction paths. On the other hand, the AFIR approach locates local minima (LMs) and transition states (TSs) of reaction paths without a guess, and therefore finds unanticipated as well as anticipated reaction paths. The AFIR method has been a

Abstract Density functional theory (DFT) and density functional theory/molecular mechanics (DFT/MM) methods are useful tools in modern homogeneous catalysis. Calculation, with its ability to characterize otherwise hardly accessible intermediates and transition states, is a key complement to experiment for the full characterization of the often intricate reaction mechanisms involved in transition metal catalysis. DFT and DFT/MM techniques have been applied to the characterization of full catalyti

Aziridines, i.e., the smallest saturated N-heterocycles, serve as useful building blocks in synthetic organic chemistry. Because of the release of the large ring strain energy accommodated in the small ring, (ca. 27 kcal/mol), aziridines undergo ring-opening reactions with a variety of nucleophiles. Therefore, among the synthetic reactions utilizing aziridines, regioselective ring-opening substitutions of aziridines with nucleophiles, such as heteroatomic nucleophiles (e.g., amines, alcohols, an

The performance of different wave-function-based and density functional theory (DFT) methods was evaluated with respect to the prediction of relative energies for gas-phase monosaccharide isomers. A test set of 58 structures was employed, representing all forms of isomerism encountered in d-aldohexoses. The set was built from eight hexopyranose epimers by deriving subsets of isomers that include hydroxymethyl rotamers, anomers, ring conformers, furanose, and open-chain forms. Each subset of isom

Density functional theory is used to explore possible mechanisms that lead to water oxidation by a bimetallic manganese catalyst developed by McKenzie and co-workers. On the basis of our calculations we propose that the key active intermediate is a mixed valent Mn(III)(μ-O)Mn(IV)-O˙ oxyl radical species, the oxyl centre being the site of nucleophilic attack by water. The mixed-valent species is in equilibrium with an isomeric diamond-core Mn(IV)(μ-O)(2)Mn(IV) structure, which acts as reservoir f

Density functional theory (DFT), combined with the artificial force-induced reaction (AFIR) method, is used to establish the mechanism of the aqueous Mukaiyama aldol reactions catalyzed by a chiral Fe(II) complex. On the bases of the calculations, we identified several thermodynamically stable six- or seven-coordinate complexes in the solution, where the high-spin quintet state is the ground state. Among them, the active intermediates for the selectivity-determining outer-sphere carbon-carbon bo

We have combined the AMOEBA09 polarizable force field with the ONIOM(QM:MM) method to rationalize binding energies and binding preferences of the OH, HCO, and CH3 radicals on crystalline water ice (Ih). ONIOM(M062X:AMOEBA09) and ONIOM(wB97XD:AMOEBA) calculations suggest that the dangling hydrogen (d-H) or dangling oxygen (d-O) on the binding sites play an important role on the binding energies. Depending on the dangling nature at the binding site, a range of binding energies is found for the OH

The reaction profile for sulfide oxidation by formally Mn(V)=O species depends critically on the electronic structure of the isolated oxidant. In cases where the ground state has dominant oxyl radical character, the oxidation occurs in sequential one-electron steps, the first of which is barrierless. In contrast, if the oxyl radical character is 'masked' in the ground state by electron transfer from either the metal or the porphyrin co-ligand, the interaction between oxidant and substrate is rep

Binding energies of the CH₃O radical on hexagonal water ice (<i>I</i>_h) and amorphous solid water (ASW) were calculated using the ONIOM(QM:MM) method. A range of binding energies is found (0.10-0.50 eV), and the average binding energy is 0.32 eV. The CH₃O radical binding on the ASW surfaces is stronger than on the <i>I</i>_h surfaces. The computed binding energies from the ONIOM(wB97X-D/def2-TZVP:AMBER) and wB97X-D/def2-TZVP methods agree quite well. Th

A Pd-catalyzed enantiospecific and regioselective ring-opening Suzuki-Miyaura arylation of aziridine-2-carboxylates was developed. The cross-coupling allows for the asymmetric preparation of enantioenriched β² -aryl amino acids, starting from commercially available enantiopure d- and l-serine esters. The mechanism and selectivity of the reaction was rationalized based on computational models.

Nowadays, computational studies are very important for the elucidation of reaction mechanisms and selectivity of complex reactions. However, traditional computational methods usually require an estimated reaction path, mainly driven by limited experimental implications, intuition, and assumptions of stationary points. However, the artificial force induced reaction (AFIR) method in the global reaction route mapping (GRRM) strategy can be used for unbiased and automatic reaction path searches for

Two transition-metal atoms bridged by hydrides may represent a useful structural motif for N₂ activation by molecular complexes and the enzyme active site. In this study, dinuclear Mo^IV -Fe^II complexes with bridging hydrides, Cp^R Mo(PMe₃ )(H)(μ-H)₃ FeCp* (2 a; Cp^R =Cp*=C₅ Me₅ , 2 b; Cp^R =C₅ Me₄ H), were synthesized via deprotonation of Cp^R Mo(PMe<sub>3</s

The performance of ONIOM(DFT:MM) methods on the structural description of molecules where intramolecular non-covalent interactions play a critical role is examined systematically and compared with that of full DFT methods, both with and without explicit dispersion corrections. The more detailed study is carried out on dithienobicyclo-[4.4.1]-undeca-3,8-diene-11-one ethylene glycol ketal molecule (CSD entry:RESVAN). Accurate description of the non-covalent interactions between two thiophene rings

The mechanism, regioselectivity, and stereospecificity of Pd/NHC-catalyzed ring-opening cross-coupling of 2-arylaziridines with arylboronic acids (Takeda et al. J. Am. Chem. Soc. 2014, 136, 8544−8547) is rationalized from density functional theory calculations. Pd(0)SIPr complex, the active species, can be formed through the reduction of (η3-cinnamyl)(Cl)Pd(II)SIPr complex, where arylboronic acid in solution plays a key role. Then the Pd(0)SIPr complex acts as the active species of the catalytic

The ONIOM scheme is one of the most popular QM/MM approaches, but its extended application has been so far hindered by the limited availability of force fields in most practical implementations. This paper describes a simple software code to overcome this limitation, and its application to three representative chemical problems. The "Shell Interface for Combining Tinker With ONIOM" (SICTWO) program gives access to all force fields available in the Tinker molecular mechanics program from a Gaussi