Interaction of Short Homopeptides of Glycine and <i>L</i>-Alanine with Fullerene C<sub>60</sub>

Basiuk, Vladimir A.; Bassiouk, María

doi:10.1166/jctn.2011.1685

Cited by 16 publications

(11 citation statements)

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“…(We already used these models in our previous studies of SWNT interactions with amino acids [33,79,80] and porphyrins [81].) They are composed of 120 (ANT) and 160 (ZNT) carbon atoms, and both have a sufficiently long tubular surface to accommodate one doxorubicin molecule without a significant contact with the closed end of spherical curvature.…”

Section: Resultsmentioning

confidence: 99%

“…The former systems comprise transition metal clusters (including nanoclusters) without [1,[3][4][5][6][7][8] and with adsorbed/chemisorbed species [9][10][11][12][13][14], metal oxides [15], and chemisorption on their surfaces [16][17][18][19], carbides [20], sulfides [21,22], and their adsorption properties [23][24][25], relatively simple transition metal coordination complexes [2], organometallic compounds [26][27][28], as well as large supramolecular species [29,30]. Also, SCF convergence can be facilitated by applying Fermi smearing when calculating light-element cluster models composed of H, C, N, and O only: a few examples are defects in nanodiamond [31], cold-plasma methanol conversion [32], and amino acid adsorption on short single-walled carbon nanotubes (SWNTs) [33]. The use of periodic models along with electron smearing was reported for such diverse systems as platinum group metals with adsorbed species and dopants [34][35][36][37][38][39][40][41][42], from atoms to rather complex molecules adsorbed on other transition metals …”

Section: Introductionmentioning

confidence: 99%

“…The interaction of a large variety of chemical species with carbon nanotube models [68,69] often exemplifies the difficult cases of SCF convergence, for example, in the case of amino acid adsorption on short SWNTs [33]. Appealing to the use of electron smearing makes it necessary to analyze (i) how the smearing can affect calculation results and (ii) what are the ''reasonable" values providing closest results to the ones obtained by means of ''no smearing" (that is, Fermi occupation) calculations.…”

Section: Introductionmentioning

confidence: 99%

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Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

Basiuk

2011

Int J of Quantum Chemistry

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To address the choice of an appropriate value of electron smearing to facilitate self-consistent field (SCF) convergence, we studied the interaction of doxorubicin with short armchair and zigzag single-walled carbon nanotube models with closed caps, at the PWC/DNP level of density functional theory. By gradually reducing the electron smearing value from a large and most commonly used one of 0.005 Ha to zero (Fermi occupation), we monitored the changes in close contacts between the interacting species, total energy of the molecular system, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy and isosurfaces, HOMO-LUMO gap energy, and plots of electrostatic potential. It became evident that the commonly used smearing values of !0.001 Ha can alter the results significantly (for example, by one order of magnitude for HOMO-LUMO gap energy). We suggest the setting of electron smearing value at 0.0001 Ha, which does not imply too high computation cost and can guarantee the results close to the ones obtained with Fermi occupation.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

Basiuk

2011

Int J of Quantum Chemistry

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“…This force field produces an ideal planar geometry for the graphene sheet model, as well as the most realistic optimized geometry of H 2 TPP in terms of the dihedral angles between C-C bonds of porphine and C 6 H 5 rings. 39 A defective HOPG surface was simulated by a graphene sheet slightly curved at the middle, representing a structure that might have been caused by a subsuperficial step edge. The sheet employed in the simulations was obtained as following (summarized in Fig.…”

Section: Methodsmentioning

confidence: 99%

Theoretical Analysis of the Effect of Surface Defects on Porphyrin Adsorption and Self-Assembly on Graphite

Bassiouk¹,

Álvarez‐Zauco²,

Basiuk³

2012

j comput theor nanosci

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Previous scanning tunneling microscopy (STM) observations of porphyrin submonolayers deposited onto highly ordered pyrolytic graphite (HOPG) repeatedly detected the formation of self-assembled porphyrin ribbons. An important observation was that these nano-sized ribbons were frequently found in contact with topological defects in graphite; in particular, this was the case of mesotetraphenylporphine (H 2 TPP), its nickel(II) and cobalt(II) complexes, and hemin. These STM results led us to suggest that the modification in the electronic structure of HOPG caused by the presence of topological (e.g., surface curvature) and oxidized defects, might result in the preferential adsorption of porphyrin molecules, therefore serving as the starting points or nucleation sites for the self-assembled ribbons. In order to support this possibility, we performed first-approach theoretical calculations with both molecular mechanical (MM + force field) and density functional theory (DFT; PWC/DN theoretical level) methods to simulate two different kinds of defects on the graphene surface, and analyze their effects on the adsorption of H 2 TPP as a model porphyrin molecule.

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“…In electrochemical nanointerface [15][16][17][18][19][20][21] based biosensors, linearity, a basic characteristic parameter, can be calibrated by knowing the enzyme kinetic parameter V max because it gives information about the saturation state. If the saturation state is attained at high substrate concentration, then its corresponding linear part will be high.…”

Section: Theorymentioning

confidence: 99%

Estimation of Michaelis-Meneten Constant and Maximum Rate of Reaction: A Nonlinear Approach

Nesakumar¹,

Sethuraman²,

Krishnan³

et al. 2014

j comput theor nanosci

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Precise estimation of Michaelis-Menten constant (K m and maximum rate of reaction (V max is very significant in studying enzyme inhibition as well as the catalytic efficiency of the immobilized enzyme in electrochemical nanointerface based biosensors. Generally linear regression models such as Lineweaver-Burk plot, Eadie-Hosftee plot, Eadie-Scatchard plot and Hanes-Woolf plot have been used to estimate enzyme kinetic parameters. But, the disadvantage of using linear regression plots is changing error statistics. As an alternative to linear regression models, three nonlinear regression models namely Gauss Newton plot, Chi Square plot and Levenberg-Marquardt fit (LVM) have been used, which fits the data by successive iterations. In this work, a sample data of lactate detecting electrochemical biosensor (Au/Nano-ZnO/LDH) has been considered for the precise estimation of K m and V max by employing nonlinear mathematical tools. Finally regression, residual, standard deviation, coefficient of variation, Chi Square, residual sum of squares and percent average relative error analyses are carried out on the adapted nonlinear mathematical models to choose optimized Michaelis-Menten equation.

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Interaction of Short Homopeptides of Glycine and L-Alanine with Fullerene C₆₀

Cited by 16 publications

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Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

Theoretical Analysis of the Effect of Surface Defects on Porphyrin Adsorption and Self-Assembly on Graphite

Estimation of Michaelis-Meneten Constant and Maximum Rate of Reaction: A Nonlinear Approach

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Interaction of Short Homopeptides of Glycine and L-Alanine with Fullerene C60

Cited by 16 publications

References 0 publications

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

Theoretical Analysis of the Effect of Surface Defects on Porphyrin Adsorption and Self-Assembly on Graphite

Estimation of Michaelis-Meneten Constant and Maximum Rate of Reaction: A Nonlinear Approach

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Interaction of Short Homopeptides of Glycine and L-Alanine with Fullerene C₆₀