The adsorption of a glycine molecule on a model silica surface terminated by an isolated hydroxyl group has been studied ab initio using a double-zeta polarized Gaussian basis set, the hybrid B3LYP functional, and a full periodic treatment of the silica surface/glycine system. The hydroxylated silica surface has been simulated using either a 2D slab or a single polymer strand cut out from the ( 001) surface of an all-silica edingtonite. A number of B3LYP-optimized structures have been found by docking glycine on the silica surface exploiting all possible hydrogen bond patterns. Whereas glycine is generally adsorbed in its neutral form, two structures show glycine adsorbed as a zwitterion, the surface playing the role of a "solid solvent" whereas intrastrand hydrogen bond cooperativity stabilizes the zwitterions. The adsorbed zwitterionic structures are no longer formed at a lower glycine coverage as simulated by enlarging the unit cell so as to break intrastrand hydrogen bonds, showing the importance of H-bond cooperativity in stabilizing the zwitterionic forms. Each structure has been characterized by computing its harmonic vibrational spectrum at the point, which also allowed us to calculate the free energy of adsorption. The experimental infrared features of chemical-vapor-deposited glycine on a silica surface are in agreement with those computed for glycine adsorbed in its neutral form and engaging three hydrogen bonds with the surface silanols, two of them involving the C=O bond and one originating from the glycine OH group. The NH2 group plays only a minor role as a weak hydrogen bond donor

Rimola, A., Sodupe, M., Tosoni, S., Civalleri, B., Ugliengo, P. (2006). Interaction of glycine with isolated hydroxyl groups at the silica surface: First principles B3LYP periodic simulation. LANGMUIR, 22(15), 6593-6604 [10.1021/la0610203].

Interaction of glycine with isolated hydroxyl groups at the silica surface: First principles B3LYP periodic simulation

Tosoni, S;
2006

Abstract

The adsorption of a glycine molecule on a model silica surface terminated by an isolated hydroxyl group has been studied ab initio using a double-zeta polarized Gaussian basis set, the hybrid B3LYP functional, and a full periodic treatment of the silica surface/glycine system. The hydroxylated silica surface has been simulated using either a 2D slab or a single polymer strand cut out from the ( 001) surface of an all-silica edingtonite. A number of B3LYP-optimized structures have been found by docking glycine on the silica surface exploiting all possible hydrogen bond patterns. Whereas glycine is generally adsorbed in its neutral form, two structures show glycine adsorbed as a zwitterion, the surface playing the role of a "solid solvent" whereas intrastrand hydrogen bond cooperativity stabilizes the zwitterions. The adsorbed zwitterionic structures are no longer formed at a lower glycine coverage as simulated by enlarging the unit cell so as to break intrastrand hydrogen bonds, showing the importance of H-bond cooperativity in stabilizing the zwitterionic forms. Each structure has been characterized by computing its harmonic vibrational spectrum at the point, which also allowed us to calculate the free energy of adsorption. The experimental infrared features of chemical-vapor-deposited glycine on a silica surface are in agreement with those computed for glycine adsorbed in its neutral form and engaging three hydrogen bonds with the surface silanols, two of them involving the C=O bond and one originating from the glycine OH group. The NH2 group plays only a minor role as a weak hydrogen bond donor
Articolo in rivista - Articolo scientifico
PEPTIDE-BOND FORMATION; MOLECULAR-DYNAMICS SIMULATIONS; HARTREE-FOCK; GRADIENTS; AB-INITIO; BIOCHEMICAL EVOLUTION; CRYSTAL CODE; AMINO-ACIDS; L-LYSINE; ADSORPTION; SYSTEMS
English
2006
22
15
6593
6604
none
Rimola, A., Sodupe, M., Tosoni, S., Civalleri, B., Ugliengo, P. (2006). Interaction of glycine with isolated hydroxyl groups at the silica surface: First principles B3LYP periodic simulation. LANGMUIR, 22(15), 6593-6604 [10.1021/la0610203].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/197690
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