Design rules for metal binding biomolecules: understanding of amino acid adsorption on platinum crystallographic facets from density functional calculations

Ramakrishnan, Sathish; Martin, Marta; Cloître, Thierry; Firlej, Lucyna; Gergely, Csilla

doi:10.1039/c4cp05112b

Cited by 20 publications

(14 citation statements)

References 30 publications

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“…This method is modified with the use of capping or templating agents which aid in modifying the shape of a NPs by adsorbing on the specific facet of a metal oxide crystal [24].…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Biosynthesis of ZnO nanoparticles using Jacaranda mimosifolia flowers extract: Synergistic antibacterial activity and molecular simulated facet specific adsorption studies

Sharma

Sabela

Kanchi

et al. 2016

Journal of Photochemistry and Photobiology B: Biology

152

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The naturally occurring biomolecules present in the plant extracts have been identified to play an active role in the single step formation of nanoparticles with varied morphologies and sizes which is greener and environmentally benign. In the present work, spherical zinc oxide nanoparticles (ZnO NPs) of 2-4nm size were synthesized using aqueous extract of fallen Jacaranda mimosifolia flowers (JMFs), treated as waste. The microwave assisted synthesis was completed successfully within 5min. Thereafter, phase identification, morphology and optical band gap of the synthesized ZnO NPs were done using X-ray diffraction (XRD), high resolution transmission electron microscopy (HRTEM) and UV-Visible spectroscopy techniques. The composition of JMFs extract was analyzed by gas chromatography-mass spectrometry (GC-MS) and the ZnO NPs confirmation was further explored with fourier transform infrared spectroscopy (FTIR). The GC-MS results confirmed the presence of oleic acid which has high propensity of acting as a reducing and capping agent. The UV-Visible data suggested an optical band gap of 4.03eV for ZnO NPs indicating their small size due to quantum confinement. Further, facet specific adsorption of oleic acid on the surface of ZnO NPs was studied computationally to find out the impact of biomolecules in defining the shape and size of NPs. The viability of gram negative Escherichia coli and gram positive Enterococcus faecium bacteria was found to be 48% and 43%, respectively at high concentration of NPs.

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“…This method is modified with the use of capping or templating agents which aid in modifying the shape of a NPs by adsorbing on the specific facet of a metal oxide crystal [24].…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Biosynthesis of ZnO nanoparticles using Jacaranda mimosifolia flowers extract: Synergistic antibacterial activity and molecular simulated facet specific adsorption studies

Sharma

Sabela

Kanchi

et al. 2016

Journal of Photochemistry and Photobiology B: Biology

152

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“…This enabled us to identify the conformation of the peptide upon adsorption and the amino acids that are responsible for facet specificity. We also found the bearing of adsorption through density of states by QM simulations with the amino acids responsible for specific‐facet specificity . In case of metals, the adsorption of peptides to the surface was mainly driven by polar and aromatic amino acids and crystallographic surface morphology.…”

Section: Understanding Interactions At the Interfacesmentioning

confidence: 71%

“…In the case of protein–surface interactions, most of the DFT simulation studies are limited to a single amino acid or small di‐ and tri‐peptide with a few hundred surface atoms . However, it can provide meaningful data for parameterizing MM force fields (FFs).…”

Section: Molecular Simulation Methods and Force Fieldsmentioning

confidence: 99%

“…Several studies addressed the interactions at the amino acid level to understand the macromolecular picture, i.e., at the level of proteins. Even at the level of amino acids, QM calculations are computationally demanding, and have performed only for a few amino acids . Ab initio methods address the exchange and dispersion effects in adsorbate‐metal adsorption, but empirical FF does not fully account for all contributions.…”

Section: Understanding Interactions At the Interfacesmentioning

confidence: 99%

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Organic–inorganic interface simulation for new material discoveries

Ramakrishnan

Zhu

Gergely

2016

WIREs Comput Mol Sci

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International audienceOrganic–inorganic interactions are of high importance in several biological pro- cesses and in modern nanobiotechnological applications. Despite its signifi- cance in interface sciences, the basic mechanism of biomolecules’ specific binding to a surface is still not well understood. Current experimental methods have not reached the level either to follow the dynamics of interactions at the picosecond scale or to observe the surface morphology at the nanoscale level. The increasing interest in bio-interfaces particularly for engineering applica- tions demands proteins or peptides to be designed to recognize the inorganic surface with high specificity. Molecular simulation has been well adopted in the past couple of decades to decipher the protein–surface interactions at differ- ent levels of time and length scales. Several molecular simulation methods such as quantum mechanics, atomistic, and coarse grain simulations were employed in this domain of research, but the continuous improvements in interfacial force field (FF) development, availability of experimental data and new sampling methods make the atomistic simulation more attractive due to the offered accu- rate representation of protein adsorption behavior at the atomic level. However, the exactitude of such simulations entirely depends on the applied FF para- meters, conformational sampling, and the solvation effects. In this overview, we briefly summarize the applicability of different simulation methods and of interface FFs. We also present the recent advances in the simulation of protein– surface interactions, and the challenges posed by the current simulation meth- ods to reproduce the exact phenomenon. Future directions in this research field are also discussed

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“…Serving as a component of an engine for design of new inhibitors (i.e., high throughput computational design) [5,6] c.…”

mentioning

confidence: 99%

Interaction of Model Inhibitor Compounds with Minimalist Cluster Representations of Hydroxyl Terminated Metal Oxide Surfaces

Taylor¹,

Kurapati

Mondal³

2018

Metals

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Abstract:The computational modeling of corrosion inhibitors at the level of molecular interactions has been pursued for decades, and recent developments are allowing increasingly realistic models to be developed for inhibitor-inhibitor, inhibitor-solvent and inhibitor-metal interactions. At the same time, there remains a need for simplistic models to be used for the purpose of screening molecules for proposed inhibitor performance. Herein, we apply a reductionist model for metal surfaces consisting of a metal cation with hydroxide ligands and use quantum chemical modeling to approximate the free energy of adsorption for several imidazoline class candidate corrosion inhibitors. The approximation is made using the binding energy and the partition coefficient. As in some previous work, we consider different methods for incorporating solvent and reference systems for the partition coefficient. We compare the findings from this short study with some previous theoretical work on similar systems. The binding energies for the inhibitors to the metal hydroxide clusters are found to be intermediate to the binding energies calculated in other work for bare metal vs. metal oxide surfaces. The method is applied to copper, iron, aluminum and nickel metal systems.

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Design rules for metal binding biomolecules: understanding of amino acid adsorption on platinum crystallographic facets from density functional calculations

Cited by 20 publications

References 30 publications

Biosynthesis of ZnO nanoparticles using Jacaranda mimosifolia flowers extract: Synergistic antibacterial activity and molecular simulated facet specific adsorption studies

Biosynthesis of ZnO nanoparticles using Jacaranda mimosifolia flowers extract: Synergistic antibacterial activity and molecular simulated facet specific adsorption studies

Organic–inorganic interface simulation for new material discoveries

Interaction of Model Inhibitor Compounds with Minimalist Cluster Representations of Hydroxyl Terminated Metal Oxide Surfaces

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