Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

Maeda, Satoshi; Harabuchi, Yu; Ôno, Y.; Taketsugu, Tetsuya; Morokuma, Keiji

doi:10.1002/qua.24757

Cited by 329 publications

(281 citation statements)

References 181 publications

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“…Intrinsic reaction coordinates (IRC) calculations [81] were performed for all TS species at the same level to confirm that anticipated reagent (R) and product (P) are connected to TS on potential energy surface. The products of the Met-OO* addition to antioxidant radical in para-position were optimized at level II.…”

Section: Methodsmentioning

confidence: 99%

Antioxidant Properties of Kynurenines: Density Functional Theory Calculations

et al. 2016

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Kynurenines, the main products of tryptophan catabolism, possess both prooxidant and anioxidant effects. Having multiple neuroactive properties, kynurenines are implicated in the development of neurological and cognitive disorders, such as Alzheimer's, Parkinson's, and Huntington's diseases. Autoxidation of 3-hydroxykynurenine (3HOK) and its derivatives, 3-hydroxyanthranilic acid (3HAA) and xanthommatin (XAN), leads to the hyperproduction of reactive oxygen species (ROS) which damage cell structures. At the same time, 3HOK and 3HAA have been shown to be powerful ROS scavengers. Their ability to quench free radicals is believed to result from the presence of the aromatic hydroxyl group which is able to easily abstract an electron and H-atom. In this study, the redox properties for kynurenines and several natural and synthetic antioxidants have been calculated at different levels of density functional theory in the gas phase and water solution. Hydroxyl bond dissociation enthalpy (BDE) and ionization potential (IP) for 3HOK and 3HAA appear to be lower than for xanthurenic acid (XAA), several phenolic antioxidants, and ascorbic acid. BDE and IP for the compounds with aromatic hydroxyl group are lower than for their precursors without hydroxyl group. The reaction rate for H donation to *O-atom of phenoxyl radical (Ph-O*) and methyl peroxy radical (Met-OO*) decreases in the following rankings: 3HOK ~ 3HAA > XAAOXO > XAAENOL. The enthalpy absolute value for Met-OO* addition to the aromatic ring of the antioxidant radical increases in the following rankings: 3HAA* < 3HOK* < XAAOXO* < XAAENOL*. Thus, the high free radical scavenging activity of 3HAA and 3HOK can be explained by the easiness of H-atom abstraction and transfer to O-atom of the free radical, rather than by Met-OO* addition to the kynurenine radical.

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Section: Methodsmentioning

confidence: 99%

Antioxidant Properties of Kynurenines: Density Functional Theory Calculations

et al. 2016

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“…37 The VRT point can be located unequivocally along the intrinsic reaction coordinate (IRC) of reactions that involve bifurcations. 38 Figure 2b shows the plot of energies of points along the forward IRC. To locate approximately the VRT point, we took every point along the IRC and computed the projected frequencies for vibrations perpendicular to the path.…”

Section: Scheme 2 Model Reaction Scheme and Computed Reaction Free Ementioning

confidence: 98%

Transannular [6 + 4] and Ambimodal Cycloaddition in the Biosynthesis of Heronamide A

Patel

Houk

2015

J. Am. Chem. Soc.

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The transannular [6 + 4] cycloaddition proposed as a step in the biosynthesis of heronamide A has been modeled using density functional theory. The proposed cycloaddition is highly stereoselective, affording a single product. The reaction proceeds through an ambimodal transition state that directly leads to a [4 + 2] adduct in addition to the observed [6 + 4] adduct. Interconversion of these adducts is possible via a facile Cope rearrangement. The [6 + 4] adduct is thermodynamically more stable than the [4 + 2] adduct by 5.2 kcal mol(-1) due to a combination of the ring and steric strain in the [4 + 2] product. The results strongly support the plausibility of the proposed transannular [6 + 4] cycloaddition in the biogenesis of heronamide A and may provide insights to designing substrates that selectively undergo [6 + 4] cycloaddition to form unbridged 10-membered rings.

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“…This is a case of bifurcation of the reaction pathway. [9][10][11][12][13][14][15] Very recently, trifurcation of the reaction pathway was reported, 16 which suggests the existence a) Author to whom correspondence should be addressed. Electronic mail:…”

Section: Introductionmentioning

confidence: 99%

Analyses of bifurcation of reaction pathways on a global reaction route map: A case study of gold cluster Au5

Harabuchi

Ôno

Maeda

et al. 2015

The Journal of Chemical Physics

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Articles you may be interested inA global reaction route map is generated for Au 5 by the anharmonic downward distortion following method in which 5 minima and 14 transition states (TSs) are located. Through vibrational analyses in the 3N − 7 (N = 5) dimensional space orthogonal to the intrinsic reaction coordinate (IRC), along all the IRCs, four IRCs are found to have valley-ridge transition (VRT) points on the way where a potential curvature changes its sign from positive to negative in a direction orthogonal to the IRC. The detailed mechanisms of bifurcations related to the VRTs are discussed by surveying a landscape of the global reaction route map, and the connectivity of VRT points and minima is clarified. Branching of the products through bifurcations is confirmed by ab initio molecular dynamics simulations starting from the TSs. A new feature of the reaction pathways, unification, is found and discussed. C 2015 AIP Publishing LLC. [http://dx

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Intrinsic reaction coordinate: Calculation, bifurcation, and automated search

Cited by 329 publications

References 181 publications

Antioxidant Properties of Kynurenines: Density Functional Theory Calculations

Antioxidant Properties of Kynurenines: Density Functional Theory Calculations

Transannular [6 + 4] and Ambimodal Cycloaddition in the Biosynthesis of Heronamide A

Analyses of bifurcation of reaction pathways on a global reaction route map: A case study of gold cluster Au5

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