scholarly journals The Adhesion Mechanism of Marine Mussel Foot Protein: Adsorption of L-Dopa onα- and β-Cristobalite Silica Using Density Functional Theory

2017 ◽  
Vol 2017 ◽  
pp. 1-6 ◽  
Author(s):  
Shabeer Ahmad Mian ◽  
Younas Khan
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Basic Mechanism ◽  
Dispersion Energy ◽  
Marine Mussel ◽  
Functional Theory ◽  
Adhesion Mechanism ◽  
Silica Surfaces ◽  
Marine Mussels ◽  
Mussel Foot Protein

Marine mussels strongly adhere to various surfaces and endure their attachment under a variety of conditions. In order to understand the basic mechanism involved, we study the adsorption of L-dopa molecule on hydrophilic geminal and terminal isolated silanols of silica (001) surface. High content of modified amino acid L-dopa is found in the glue-like material secreted by the mussels through which it sticks to various surfaces under water. To understand the adsorption behavior, we have made use of periodic Density Functional Theory (DFT) study. The L-dopa molecule adheres to silica surfaces terminated with geminal and terminal silanols via its catechol part. In both cases, the adhesion is achieved through the formation of 4 H-bonds. A binding energy of 29.48 and 31.67 kcal/mol has been estimated, after the inclusion of dispersion energy, for geminal and terminal silanols of silica, respectively. These results suggest a relatively stronger adhesion of dopa molecule for surface with terminal isolated silanols.

Adhesion of Organic Molecules on Silica Surfaces: A Density Functional Theory Study

2016 ◽  
Vol 121 (1) ◽  
pp. 392-401 ◽  
Author(s):  
Mathew E. McKenzie ◽  
Sushmit Goyal ◽  
Sung Hoon Lee ◽  
Hyun-Hang Park ◽  
Elizabeth Savoy ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Organic Molecules ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Silica Surfaces

Binding Energies of Organic Charge-Transfer Complexes Calculated by First-Principles Methods

1998 ◽  
Vol 63 (8) ◽  
pp. 1223-1244 ◽  
Author(s):  
Cordula Rauwolf ◽  
Achim Mehlhorn ◽  
Jürgen Fabian
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Ground State ◽  
Density Functional ◽  
Binding Energies ◽  
Basis Set ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Basis Set Superposition Error ◽  
Donor And Acceptor

Weak interactions between organic donor and acceptor molecules resulting in cofacially-stacked aggregates ("CT complexes") were studied by second-order many-body perturbation theory (MP2) and by gradient-corrected hybrid Hartree-Fock/density functional theory (B3LYP exchange-correlation functional). The complexes consist of tetrathiafulvalene (TTF) and related compounds and tetracyanoethylene (TCNE). Density functional theory (DFT) and MP2 molecular equilibrium geometries of the component structures are calculated by means of 6-31G*, 6-31G*(0.25), 6-31++G**, 6-31++G(3df,2p) and 6-311G** basis sets. Reliable molecular geometries are obtained for the donor and acceptor compounds considered. The geometries of the compounds were kept frozen in optimizing aggregate structures with respect to the intermolecular distance. The basis set superposition error (BSSE) was considered (counterpoise correction). According to the DFT and MP2 calculations laterally-displaced stacks are more stable than vertical stacks. The charge transfer from the donor to the acceptor is small in the ground state of the isolated complexes. The cp-corrected binding energies of TTF/TCNE amount to -1.7 and -6.3 kcal/mol at the DFT(B3LYP) and MP2(frozen) level of theory, respectively (6-31G* basis set). Larger binding energies were obtained by Hobza's 6-31G*(0.25) basis set. The larger MP2 binding energies suggest that the dispersion energy is underestimated or not considered by the B3LYP functional. The energy increases when S in TTF/TCNE is replaced by O or NH but decreases with substitution by Se. The charge-transferred complexes in the triplet state are favored in the vertical arrangement. Self-consistent-reaction-field (SCRF) calculations predicted a gain in binding energy with solvation for the ground-state complex. The ground-state charge transfer between the components is increased up to 0.8 e in polar solvents.

Density Functional Theory Study of Catechol Adhesion on Silica Surfaces

2010 ◽  
Vol 114 (48) ◽  
pp. 20793-20800 ◽  
Author(s):  
Shabeer A. Mian ◽  
Leton C. Saha ◽  
Joonkyung Jang ◽  
Lu Wang ◽  
Xingfa Gao ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Silica Surfaces

Nonempirical density-functional theory for van der Waals interactions

2010 ◽  
Vol 88 (11) ◽  
pp. 1057-1062 ◽  
Author(s):  
Axel D. Becke ◽  
Alya A. Arabi ◽  
Felix O. Kannemann
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Local Density ◽  
Van Der Waals ◽  
Van Der Waals Complexes ◽  
Basis Sets ◽  
Generalized Gradient ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Grid Based

In previous work, Kannemann and Becke [ J. Chem. Theory Comput. 5, 719 (2009) and J. Chem. Theory Comput. 6, 1081 (2010) ] have demonstrated that the generalized gradient approximations (GGAs) of Perdew and Wang for exchange [Phys. Rev. B 33, 8800 (1986)] and Perdew, Burke, and Ernzerhof for correlation [Phys. Rev. Lett. 77, 3865 (1996)] , plus the dispersion density functional of Becke and Johnson [J. Chem. Phys. 127, 154108 (2007)] , comprise a nonempirical density-functional theory of high accuracy for thermochemistry and van der Waals complexes. The theory is nonempirical except for two universal cutoff parameters in the dispersion energy. Our calculations so far have been grid-based and have employed the local density approximation (LDA) for the orbitals. In this work, we employ orbitals from self-consistent GGA calculations using Gaussian basis sets. The results, on a benchmark set of 65 van der Waals complexes, are similar to our grid-based post-LDA results. This work sets the stage for van der Waals force computations and geometry optimizations.

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