Comparison of Different Three-site Interaction Potentials for Liquid Acetonitrile

Guàrdia, E.; Pinzón, Reinhardt; Casulleras, J.; Orozco, Modesto; Luque, F. Javier

doi:10.1080/08927020108024509

Cited by 64 publications

(98 citation statements)

References 32 publications

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“…The second coordination shell for this pair interaction was taken place at 7.5 Å. Probability of finding C1 atom in the vicinity of the N atom was due to interactions of positively charged H atoms with the negatively charged N atom. Such coordination is observed in both three and sixsite models reported in other references 20,16,13,14 with almost the same amplitude and location. Further examination of Figure 1(a) reveals that the least interaction between C1 and N occurred at radius, 5.4 Å, where other interactions, such as C1-C2 and C1-C1, are still high enough.…”

Section: Resultssupporting

confidence: 62%

“…The second peak observed in this interaction is not significant in three-site models. 13,14,20 In contrast to the other interactions, N-N interactions take place relatively are taken place in a long distance compared with those of C1-N. Moreover, N-N interactions form a second shell that is very close to the first one.…”

Section: Resultsmentioning

confidence: 99%

“…20 Energy parameter of H and separation distance of N were based on DREIDING and set to 0.0152 kcal/mol and 3.292 Å respectively. 21 Separation distance for H was taken account as a free parameter for better agreement between the computed and experimental viscosities.…”

mentioning

confidence: 99%

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Dielectric and Transport Properties of Acetonitrile at Varying Temperatures: a Molecular Dynamics Study

Orhan

2014

Bulletin of the Korean Chemical Society

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Use of acetonitrile in electrolytes promotes better operation of supercapacitors. Recent efforts show that electrolytes containing acetonitrile can also function in a wide range of operating temperatures. Therefore, this paper addresses the dielectric relaxation processes, structure and dynamic properties of the bulk acetonitrile at various temperatures. Systems of acetonitrile were modeled using canonical ensemble and simulated by employing Molecular Dynamics method. Results show that interactions among the molecules were correlated within a cut-off radius while parallel and anti-parallel arrangements are observed beyond this radius at relatively high and low temperatures respectively. Furthermore, effects of C-C-N and C-H bending modes were greatly appreciated on the power spectral density of time rate change of dipole-dipole correlations whereas frequency shifts were observed on all modes at the lowest temperature under consideration. Linear variations with temperature were depicted for reorientation times and self-diffusion coefficients. Shear viscosity was also computed with a good accuracy within a certain range of the temperature as well.

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Section: Resultssupporting

confidence: 62%

Section: Resultsmentioning

confidence: 99%

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Dielectric and Transport Properties of Acetonitrile at Varying Temperatures: a Molecular Dynamics Study

Orhan

2014

Bulletin of the Korean Chemical Society

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“…Acetonitrile (ACN) was treated by the available united-atom model, [65] while chloroform (CHL) [66] and water (WAT, described by TIP3P) [67] parameters were taken from all-atom models.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Computational design of a lipase for catalysis of the Diels-Alder reaction

et al. 2010

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Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the Diels-Alder reaction by a modified lipase. Six variants of the versatile enzyme {\em Candida Antarctica} lipase B (CALB) have been rationally engineered {\em in silico} based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity shape and size, and can be controlled by a few rational mutations. The well-documented S105A mutation is essential to enable sufficient space in the vicinity of the oxyanion hole. Moreover, bulky residues on the edge of the active site hinders the formation of a sandwich-like near-attack conformer (NAC), and the I189A mutation is needed to obtain enough space above the face of the $\alpha$,$\beta$-double bond on the dienophile. The double mutant S105A/I189A performs quite well for two of three dienophiles. Based on binding constants and NAC energies obtained from MD simulations combined with activation energies from DFT computations, relative catalytic rates ($v_{cat}/v_{uncat}$) of up to $10^3$ are predicted.Response to Reviewers: We are happy with the favorable comments by the reviewers. We have have corrected the manuscript as suggested by reviewer 1 1. A sentence explaining catalytic promiscuity has been added. 2. A paragraph discussing the relationship between the NAC concept and the Reaction Force has been added.We have shortened the manuscript as suggested by reviewer 2. In particular, we have moved information regarding the structural relaxation of protein structure in MD simulations to the supplementary material. Abstract Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the DielsAlder reaction by a modified lipase. Six variants of the versatile enzyme Candida Antarctica lipase B (CALB) have been rationally engineered in silico based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity s...

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“…The GS geometry was then placed in a 32x32x44Å box of thermally pre-equilibrated acetonitrile (ACN) molecules, modelled with a classical, rigid, three-point interaction potential. 48 Non-bonded parameters for the complex were chosen from the UFF force field. 49 Solvent molecules overlapping the [Ru=Co] complex were removed, giving a total of 436 ACN molecules.…”

Section: Methodsmentioning

confidence: 99%

Electron Transfer and Solvent-Mediated Electronic Localization in Molecular Photocatalysis

et al. 2016

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This work provides a detailed mechanism for electron transfer in a hetero-dinuclear complex designed as a model system in which to study homogeneous molecular photocatalysis. With efficient Born-Oppenheimer Molecular Dynamics simulations, we show how intermediate, charge separated states can mediate the electron transfer. We observe how Jahn-Teller distortion effects play out in solution, when the molecule has energetically close-lying states and how this distortion is averaged out in the thermal sampling. Finally, we demonstrate how the solvent helps stabilize and localize the separated charge. The information on the electronic configuration and separate states is of key importance for designing next generation photocatalysts.

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Comparison of Different Three-site Interaction Potentials for Liquid Acetonitrile

Cited by 64 publications

References 32 publications

Dielectric and Transport Properties of Acetonitrile at Varying Temperatures: a Molecular Dynamics Study

Dielectric and Transport Properties of Acetonitrile at Varying Temperatures: a Molecular Dynamics Study

Computational design of a lipase for catalysis of the Diels-Alder reaction

Electron Transfer and Solvent-Mediated Electronic Localization in Molecular Photocatalysis

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