Accurate reaction paths using a Hessian based predictor–corrector integrator

Hratchian, Hrant P.; Schlegel, H. Bernhard

doi:10.1063/1.1724823

Cited by 840 publications

(548 citation statements)

References 35 publications

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“…Besides optimization of transition structures, this investigation involved frequency and intrinsic reaction coordinate (IRC) 74 calculations to obtain Gibbs free energies and to verify that the transition structures found connect the associated reactant and product species. To solidify the conclusions as best as possible, these calculations were performed (using an SMD description of the dichloromethane solvent) with all of the density functionals mentioned earlier.…”

Section: Methodsmentioning

confidence: 99%

Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects

Oruganti

Fang

Durbeej

2015

Phys. Chem. Chem. Phys.

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We report a systematic computational investigation of the possibility to accelerate the rate-limiting thermal isomerizations of the rotary cycles of synthetic light-driven overcrowded alkene-based molecular motors through modulation of steric interactions.Choosing as reference system a second-generation motor known to accomplish rotary motion in the MHz regime and using density functional theory methods, we propose a three-step mechanism for the thermal isomerizations of this motor and show that variation of the steric bulkiness of the substituent at the stereocenter can reduce the (already small) free-energy barrier of the rate-determining step by a further 15−17 kJ mol -1 . This finding holds promise for future motors of this kind to reach beyond the MHz regime. Furthermore, we demonstrate and explain why one particular step is kinetically favored by decreasing and another step is kinetically favored by increasing the steric bulkiness of this substituent, and identify a possible back reaction capable of impeding the rotary rate.3

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Section: Methodsmentioning

confidence: 99%

Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects

Oruganti

Fang

Durbeej

2015

Phys. Chem. Chem. Phys.

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“…The structures of the identified TSs were further investigated: the diagonalized mass-weighted Hessian matrix showed only one negative eigenvalue, revealing a first-order saddle point. To confirm the reac- 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim ChemMedChem 2014, 9, 323 -336 334 CHEMMEDCHEM FULL PAPERS www.chemmedchem.org tion path, we performed intrinsic reaction coordinate (IRC) [44] calculations in order to follow the reaction starting from the TS reaching the reactants and the products. Finally the end points of the IRC pathway were optimized, and the nature of these points was investigated, confirming that they are energy minima in the potential energy surface.…”

Section: Methodsmentioning

confidence: 99%

Synthesis, Structure–Activity, and Structure–Stability Relationships of 2‐Substituted‐N‐(4‐oxo‐3‐oxetanyl) N‐Acylethanolamine Acid Amidase (NAAA) Inhibitors

et al. 2014

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N‐Acylethanolamine acid amidase (NAAA) is a cysteine amidase that preferentially hydrolyzes saturated or monounsaturated fatty acid ethanolamides (FAEs), such as palmitoylethanolamide (PEA) and oleoylethanolamide (OEA), which are endogenous agonists of nuclear peroxisome proliferator‐activated receptor‐α (PPAR‐α). Compounds that feature an α‐amino‐β‐lactone ring have been identified as potent and selective NAAA inhibitors and have been shown to exert marked anti‐inflammatory effects that are mediated through FAE‐dependent activation of PPAR‐α. We synthesized and tested a series of racemic, diastereomerically pure β‐substituted α‐amino‐β‐lactones, as either carbamate or amide derivatives, investigating the structure–activity and structure–stability relationships (SAR and SSR) following changes in β‐substituent size, relative stereochemistry at the α‐ and β‐positions, and α‐amino functionality. Substituted carbamate derivatives emerged as more active and stable than amide analogues, with the cis configuration being generally preferred for stability. Increased steric bulk at the β‐position negatively affected NAAA inhibitory potency, while improving both chemical and plasma stability.

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“…B3LYP (30)(31)(32) and BP86 (30,33) functionals were employed in combination with split valence double-zeta, singly polarized 6-31G(d) (34,35) and DGDZVP (36, 37) basis sets. Stationary points (minima or transition states) were verified by frequency calculations, and reaction paths from transition states were identified by tracking intrinsic reaction coordinates (38,39). Solvation effects were investigated via the polarizable continuum model using the integral equation formalism (40), which is the default self-consistent reaction field method in G09.…”

Section: Methodsmentioning

confidence: 99%

Kinetics and mechanistic analysis of an extremely rapid carbon dioxide fixation reaction

Huang

Makhlynets

Tan

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

124

101

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Carbon dioxide may react with free or metal-bound hydroxide to afford products containing bicarbonate or carbonate, often captured as ligands bridging two or three metal sites. We report the kinetics and probable mechanism of an extremely rapid fixation reaction mediated by a planar nickel complex ½Ni II ðNNNÞðOHÞ 1− containing a tridentate 2,6-pyridinedicarboxamidate pincer ligand and a terminal hydroxide ligand. The minimal generalized reaction is M-OH þ CO 2 → M-OCO 2 H; with variant M, previous rate constants are ≲10 3 M −1 s −1 in aqueous solution. For the present bimolecular reaction, the (extrapolated) rate constant is 9.5 × 10 5 M −1 s −1 in N, N′-dimethylformamide at 298 K, a value within the range of k cat ∕K M ≈10 5 -10 8 M −1 s −1 for carbonic anhydrase, the most efficient catalyst of CO 2 fixation reactions. The enthalpy profile of the fixation reaction was calculated by density functional theory. The initial event is the formation of a weak precursor complex between the Ni-OH group and CO 2 , followed by insertion of a CO 2 oxygen atom into the Ni-OH bond to generate a four center Niðη 2 -OCO 2 HÞ transition state similar to that at the zinc site in carbonic anhydrase. Thereafter, the Ni-OH bond detaches to afford the Niðη 1 -OCO 2 HÞ fragment, after which the molecule passes through a second, lower energy transition state as the bicarbonate ligand rearranges to a conformation very similar to that in the crystalline product. Theoretical values of metric parameters and activation enthalpy are in good agreement with experimental values [ΔH ‡ ¼ 3.2ð5Þ kcal∕mol].nickel hydroxide | carbon dioxide-bicarbonate conversion | reaction mechanism R ecent research in this laboratory has been directed toward the attainment of synthetic analogues of the NiFe 3 S 4 active site of the enzyme carbon monoxide dehydrogenase (1, 2), which catalyzes the interconversion reactionIn the course of this work, we have prepared binuclear Ni II ∕Fe II bridged species with the intention of simulating the Ni…Fe component of the enzyme site that is the locus of substrate binding, activation, and product release (3). The nickel site in the binuclear species has been prepared separately in the form of the planar hydroxide complex ½NiðpyN 2 Me2 ÞðOHÞ 1− containing a N,N′-2,6-dimethylphenyl-2,6-pyridinedicarboxamidate dianion. Whereas bridging hydroxide ligation is common, terminal binding is not and in general is stabilized in divalent metal complexes by hydrogen bonding or by steric shielding, as is the case here. As reported recently (3), exposure of a solution of ½NiðpyN 2 Me2 ÞðOHÞ 1− to the atmosphere results in an instantaneous color change from red to red-orange. This results in the fixation of CO 2 as the bicarbonate complex ½NiðpyN 2 Me2 ÞðHCO 3 Þ 1− accompanied by the spectral changes in Fig. 1. Several features of the CO 2 fixation reaction 1 are noteworthy. The reactant is a terminal hydroxide species affording a unidentate bicarbonate (η 1 -OCO 2 H) product. Far more common is the reaction of bridged M II 2 ðμ-OHÞ 1;2 pr...

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Accurate reaction paths using a Hessian based predictor–corrector integrator

Cited by 840 publications

References 35 publications

Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects

Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects

Synthesis, Structure–Activity, and Structure–Stability Relationships of 2‐Substituted‐N‐(4‐oxo‐3‐oxetanyl) N‐Acylethanolamine Acid Amidase (NAAA) Inhibitors

Kinetics and mechanistic analysis of an extremely rapid carbon dioxide fixation reaction

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