Models for the representation of knowledge about chemical reactions

Theoretical approach to the innovative mutation of naphthalene 1,2-dioxygenase: a molecular dynamics and docking study

“…1) that 15 (29 %) of the 50 molecules were not able to interact with the active site of the enzyme (positive binding energy). In particular, molecules 8,9,13,20,28,34,35,36,42, and 45 were those with the highest binding energies. Upon examining the interactions between the 12 PAHs and the active site of NDO, we noticed that, in many cases, the various PAHs all present similar interactions with the same amino acids of the active site of the NDO (Table 2).…”

“…This database was used as a source of experimental data for all of the PAHs studied. The structures of the selected PAHs were constructed using an editing software package from Accelrys (San Diego, CA, USA) and then minimized to the nearest local minimum energy; Gasteiger charges were assigned [28], and nonpolar hydrogen atoms were fused. For the protein, the geometrical average structures as obtained from the last atomic coordinates (x,y,z) (50 ps for each MD simulation) were first minimized and then used in docking calculations.…”

Construction of a Statistical Evaluation Model Based on Molecular Centrality to Find Retrosynthetically Important Bonds in Organic Compounds

“…e) Reactions involving organometallic compounds are omitted because of the difficulty in estimating the BDEs of organometallic bonds by this method. [10] For reaction schemes satisfying the above conditions, the parameters BC, BDE, and NCC of the connecting and other bonds in the product structures were calculated as independent variables [Equations (6)- (8)]. …”

“…c) BC, BDE, and NCC were standardized to sBC, sBDE, and sNCC by Equation (9) [X i (j) in Table 1]. d) The dissimilarities of the connecting bond (j = 4 in Table 1), DIS(j,4), were calculated by Equation (10). e) Bonds with the largest DIS(j,4) (= 9.341) value were recognized (j = 14, 15, 16, 20, 21, and 22 in Table 1) and one bond (j = 4) was extracted as a nonconnecting bond.…”

“…For statistical analysis, three bond properties, bond centrality (BC), bond dissociation energy (BDE), [10] and the number of chiral centers (NCC), [11] were used as independent variables. BC is a parameter used to describe the location of bonds in a molecule, and the BDE and NCC are indices that represent the degree of synthetic accessibility and intractableness related to the asymmetric syntheses of bonds.…”