A Density Functional Theory Study of Cytosine on Au(111)

Rosa, Marta; Corni, Stefano; Felice, Rosa Di

doi:10.1021/jp305833c

Cited by 40 publications

(71 citation statements)

References 49 publications

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“…Other functionals akin to vdW-DF have been proposed to correct this deficiency (Lee et al 2010;Klimeš et al 2010Klimeš et al , 2011, and are awaiting testing and validation in the field of molecular adsorption, and specifically for protein-surface interactions. The computational overhead in using these functionals is modest, and they have also been applied to other biomolecules adsorbed on gold, such as nucleic acids (Rosa et al 2012(Rosa et al , 2014a. AIMD is also possible with these functionals, as exemplified by a recent study of the liquid water/gold interface (Nadler & Sanz, 2012).…”

Section: Morphologymentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

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197

199

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Abstract. Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time-and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

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Section: Morphologymentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

Self Cite

197

199

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“…They also proved to be responsible for a large fraction of the molecule-surface interactions; for example, according to Aradhya et al [24], 0a National Institute for Research and Development of Isotopic and Molecular Technologies, Department of Molecular and Biomolecular Physics, 65-103 Donath, 400293 Cluj-Napoca, Romania, cristian.morari@itim-cj.ro 2 Computational details DFT is employed as the first principles quantum mechanical method. It provides efficient and typically accurate estimates of the molecule-crystal binding energies, molecular dissociation, surface atom rearrangements, and the overall electronic structure of a nanoscopic system [25,26,9,27,28,29,39,40,41,42]. It is well-known that DFT with a plane-wave basis set properly models electronic properties of bulk materials with Bloch-like wave functions spreading over the entire unit cell.…”

Section: Introductionmentioning

confidence: 99%

Adsorption of small aromatic molecules on gold: a DFT localized basis set study including van der Waals effects

Buimaga-Iarinca

Morari

2014

Theor Chem Acc

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We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule-surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the gold-gold distances within the relaxed systems. Consequently, we find that by using different types of LCAO basis sets or geometric models for the adsorption of the molecules on the surface, the binding energy can vary up to 100 %. A critical analysis of the physical parameters resulting from the calculations is presented for each exchange-correlation functional.

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“…34−36 Similar tilted but near plane-parallel geometries have been proposed for cytosine and aminesubstituted aromatics adsorbed on Au(111). 37,38 In each case, lone-pair interactions of the substituents with the substrate contributed to the tilted geometry.…”

Section: Discussionmentioning

confidence: 98%

Prevailing Intermolecular Bonding for Dinitrotoluene Self-Assembled Monolayers on Au(111)

Jiang

Willis

2014

J. Phys. Chem. C

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The self-assembly of 2,4-and 2,6-dinitrotoluene was investigated on Au(111) surfaces using a combined experimental and density functional theory approach. Well-ordered monolayers were observed with rectangular unit cells commensurate with the Au substrate along the next-nearest-neighbor direction. The unit cell is made of two molecules per cell in an unusual vertical configuration, driven by a strong dipole−dipole interaction between molecules and with lesser interaction with the substrate. van der Waals density functional theory models of bonding in the molecular layer show strong intermolecular interactions that dominate over substrate interactions with cohesive energies near 24 kcal/mol. The calculations are corroborated by temperature-programmed desorption experiments and demonstrate that intermolecular interactions dominate the self-assembly of this molecular adsorption system. Both dipole−dipole and van der Waals interactions are significant contributors to the bonding, and the importance of van der Waals corrected density functional theory is shown. We argue that the molecule−molecule vs molecule−substrate interactions are controlled by the optimization of energy per unit surface area.

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A Density Functional Theory Study of Cytosine on Au(111)

Cited by 40 publications

References 49 publications

Modeling and simulation of protein–surface interactions: achievements and challenges

Modeling and simulation of protein–surface interactions: achievements and challenges

Adsorption of small aromatic molecules on gold: a DFT localized basis set study including van der Waals effects

Prevailing Intermolecular Bonding for Dinitrotoluene Self-Assembled Monolayers on Au(111)

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