DFT study of the adsorption of microsolvated glycine on a hydrophilic amorphous silica surface

DFT study of the adsorption of microsolvated glycine on a hydrophilic

amorphous silica surfacew

Dominique Costa,*ab Asma Tougerti,a Frederik Tielens,a Christel Gervais,c

Lorenzo Stievanoaand Jean Francois Lambert

a

Received 16th April 2008, Accepted 25th July 2008

First published as an Advance Article on the web 23rd September 2008

DOI: 10.1039/b806501b

Density functional theory (DFT) periodic ab initio molecular dynamics calculations are used to

study the adsorption of gaseous and microsolvated glycine on a hydroxylated, hydrophilic silica

surface. The silica model is presented and the interaction of water with surface silanols is studied.

The heat of interaction of water is higher with the associated silanols (be they terminal or geminal

ones) studied here than with isolated silanols presented in past works. Glycine is stabilized in a

parallel mode on the hydroxylated surface. Terminal silanols do not allow the stabilization of the

zwitterionic form, whereas geminal silanols do. Molecular dynamics (MD) first-principle

calculations show that microsolvated zwitterion glycine directly binds through the carboxylate

function to a surface silanol rather than through water molecules. The adsorption mode, whether

with or without additional water molecules, is parallel to the surface. The ammonium function

does not interact directly with the silanol groups but rather through water molecules. Thus, the

carboxylate and ammonium functions exhibit two different reactivities towards silanols. The

calculated free energies, taking into account the chemical potentials of water and glycine in the

gas phase, suggest the existence of a thermodynamic domain in which the glycine is present in the

gas phase as well as strongly adsorbed on specific sites of the surface.

Introduction

Mineral surfaces have been suggested, already in the late 1950s, to

play a role in the activation of amino acids polymerization that

lead to the formation of peptides in early prebiotic chemistry.1

In particular, clays and other oxides were present in large

amounts on the prebiotic earth crust after the formation of

hydrosphere, and may have played an important role in the

process of chemical evolution (ref. 2 and references therein).

The earth crust consists primarily of silicate minerals,

containing a number of metal cations (e.g.aluminium,

magnesium, calcium, iron etc.) mainly structured in frame-

works of (SiO4) tetrahedra connected by siloxane bonds. In

spite of relevant differences with natural silicates, the study of

the adsorption and reactivity of amino acids on a pure silica

system can be considered as a ‘‘model’’ system for studying the

role that such surfaces may have played in the activation of

peptide bond formation.3

For oxides such as silica, alumina or iron oxides, molecular-

level studies remain scarce, even though it would be desirable

to know, not only if such surfaces can exhibit significant

selectivities (maybe even molecular recognition phenomena)

for different biomolecules going from amino acids to proteins,

but also whether the structure of the adsorption site may

influence the reactivity of adsorbed biomolecules.

Recently, theoretical ab initio tools have been successfully

used to investigate the mode of interaction of small biofunctions

with oxide and sulfide surfaces, in particular the adsorption of:

glycine on a dry (110) rutile surface,4 cysteine and serine on a

dry (110) and a hydroxylated (100) rutile surface,5 glycine on

pyrite,6 on alumina7 and on crystalline silica.8,9

We have undertaken a joint experimental and theoretical

study of the adsorption of glycine on amorphous silica surfaces

from the point of view of the surface, using knowledge pre-

viously gained on the molecular identification of surface func-

tional groups (such as silanols, silanolates, ‘‘nests’’ of

silanols. . .) to better characterize their interaction with amino

acids, both from the aqueous10 and from the vapor phase.11 We

showed that glycine from the aqueous phase binds with specific

surface sites at a coverage of 0.8 glycine nm�2 (10% of the

physical monolayer). In the theoretical part of our work, we

presented B3LYP results, obtained with minimal clusters of

glycine interacting with a silica surface, with and without ref.

11–13 the presence of water molecules. It was found that glycine

from the gas phase may form H-bond rings with silanols, and

that additional water molecules are needed to stabilize zwitter-

ionic glycine on the surface ref. 11 and 12. We focused our

attention on comparing calculated and experimental vibration

frequencies, namely the nCOO and dHNH modes. A precise

characterization of the glycine adsorption site was difficult,

principally due to the overlapping of frequencies with dHOH

of residual water, and also to the coupling of those frequencies

a Laboratoire de Reactivite de Surface, Universite Pierre et MarieCurie—Paris 6, 4, Place Jussieu, F-75252 ParisCedex 05 France

b Laboratoire de Physico-Chimie des Surfaces, ENSCP, 11 rue P. etM. Curie, 75005 Paris, France. E-mail: [email protected]

c Laboratoire de Chimie de la Matiere Condensee, Universite Pierre etMarie Curie—Paris 6, 4, Place Jussieu, F-75252 ParisCedex 05Francew Electronic supplementary information (ESI) available: Furthersimulation details. See DOI: 10.1039/b806501b

6360 | Phys. Chem. Chem. Phys., 2008, 10, 6360–6368 This journal is �c the Owner Societies 2008

PAPER www.rsc.org/pccp | Physical Chemistry Chemical Physics

with those of water molecules. Therefore, further theoretical

efforts are necessary to gain more precise insights into the

specific adsorption site.

However, the cluster calculations performed do not take into

account the long-range interactions and the information on the

constraints induced by the surface. Density functional theory

(DFT) periodic calculations of glycine adsorption on a crystal-

line silica were also performed.9 It was shown that the heat of

interaction of glycine with an isolated silanol is 56.9 kJ mol�1.9

However, isolated silanols are expected from experimental

results to exhibit a different reactivity versus probe molecules

than associated ones.14,15 H-Bonded silanols in silanol nests

have been suggested to be more reactive to water than isolated

ones and to allow water clustering.14–16 In addition, our own

works suggest that glycine, a hydrophilic amino-acid, should

adsorb on a silanol nest.11–13

We thus present here a study of the adsorption of glycine

(neutral or zwitterionic) on a model of silica surface exhibiting

OH clustering on the surface and also different types of OH

groups (terminal and geminal).

The scope of the present work is to explore briefly the

water/silica, glycine/silica, and microsolvated glycine/silica

interfaces at low coverages of amino acid (AA) on the surface,

as is found experimentally. In addition, we calculated thermo-

dynamical values (DG1) of the interface as a function of the

temperature and partial pressure, and we deduce desorption

temperatures of water and glycine from the surface.

Computational details

Every geometry optimization and minimization of the total

energy has been performed using the VASP code.17,18 In the

periodic density functional theory framework used,

the Kohn–Sham equations have been solved by means of the

generalized gradient approximation (GGA-PW91) proposed

by Perdew and Wang.19,20 The electron–ion interaction was

described by the projector augmented-wave method

(PAW).21,22 The plane-wave expansion was truncated at a

cut-off energy of 400 eV.

Because of the large cell size, the calculations were

performed at the G point for the Brillouin-zone integration.

Ab initio molecular dynamics (MD) runs were also performed

to scan the possible conformations of the system at room

temperature. The time step was set at 1.5 fs and run; we

considered several starting conformations (but no statistic was

performed on the starting conformations) and the run was

stopped when an average stable conformation was reached

during 500 fs or more; we used a micro-canonical ensemble in

the NVE approach. To avoid fluctuations due to the large time

step chosen, the mass of hydrogen atom was set to 3.

The amorphous silica surface model is inspired on the model of

Masini and Bernasconi.23 After relaxation the obtained surface is

16.8 � 9.3 A with a slab thickness varying from 5.2 to 8.2 A,

corresponding to a three layers slab (see Fig. 1a). The obtained

surface is described in section A of the results section. From this

model, the two bottom layers were fixed at the optimized

geometry positions, whereas the surface layer was relaxed.

We introduced one glycine molecule in the supercell,

obtaining a glycine coverage of 0.6 molecule nm�2, a value

comparable with the 0.8 mol nm�2 observed experimentally at

low glycine activity. In these conditions, lateral interactions

between two glycine molecules in neighboring cells are

avoided. Typically, the glycine/water molecules and the

glycine/water complexes were optimized separately and then

introduced in the supercell, and the interface was let free to

relax. We verified that the adsorption energy did not change

significantly between relaxation of one silica layer and relaxa-

tion of two silica layers. A 20 A vacuum space in the supercell

was added in order to avoid interaction between the surface

cells along the z-axes. A dipolar correction was introduced in

the axis perpendicular to the surface.

In a preliminary study, the GGA PW91 results obtained

with VASP on the interaction of glycine with water molecules

were compared with results obtained at a theoretical level

allowing a better description of hydrogen-bonded systems

(MP2 and B3LYP with 6-311++G** basis set), as studied

and described in detail experimentally by Stepanian et al.24

and Ramaekers et al.25 and theoretically by Ramaekers et al.25

and Aikens and Gordon26

More precisely, we found that PW91 available in VASP

overestimates the H bond by around 10%, a result in line with

recent studies on H bonded systems;27 consequently, the

NG (glycine) to ZG (zwitterion) transition, occurs for 4 water

molecules (instead of 5 using B3LYP), as reported in

Table 1. We thus perform our calculations keeping in mind

this systematic overestimation. As we compare different

configurations of the same molecule on the surface, we believe

the comparative trends remain valid.

Fig. 1 Amorphous silica surface obtained after a standard geometry

optimization—(a) above view, (b) side view—exhibiting the three silica

layers. Red: oxygen of silanol. Large light gray: oxygen in siloxane

bridge. Small dark grey: Si atoms.

This journal is �c the Owner Societies 2008 Phys. Chem. Chem. Phys., 2008, 10, 6360–6368 | 6361

The energies of interaction/adsorption of glycine on the

surface were calculated following different reactions: First,

the neutral glycine NG was considered as the reactant; the

calculated energy

D1E = E(G, Sil) � E(NG) � E(Sil) (1)

where E(NG) and E(Sil) are the total electronic energies of glycine

(neutral) and silica surface obtained after separate geometry

optimization and E(G, Sil) is the energy of the optimized (glycine

+ silica) system with glycine adsorbed on the silica surface.

From the electronic energy, the free energy of the water/silica

and glycine/silica interfaces under known thermodynamic

conditions may be estimated following the approximations

used in ref. 28. We consider that the water (glycine)/silica

system is in contact with a gaseous water (glycine) reservoir.

The approximations done in ref. 28, originating from Kaxiras

et al.29 and Qian et al.,30 consist in neglecting the variation of

the chemical potentials of the surfaces with the adsorption and

considering the gas phase as a perfect gas. In the proposed

scheme, the free energy of adsorption is the electronic energy

calculated at 0 K, minus the variation of the chemical potential

of glycine (including the ZPE correction)

DG = E(0) � [(DHG � TSG(T)] + RTln(P/P1) (2)

where E is the energy of reaction calculated at 0 K, DHG and

SG(T) are the enthalpy and entropy of gaseous neutral glycine,

calculated with the Gaussian03 code31 as a function of the

temperature, P is the partial pressure of glycine vapor and

P1 is the standard pressure (1 bar).

For a given (T,P) pair, the sign of DG indicates if the adsorption

of glycine will occur or if glycine is more stable in the gas phase:

when DG o 0, glycine is more stable when adsorbed on silica;

when DG 4 0, glycine remains in the gas phase.

Only the most relevant configurations are given in the body

of the article. Other configurations are added in the ESI.wAll results files are available by contacting the author at

[email protected].

Results

A Hydroxylated silica surface—choice, description of the

model and geometry optimization

The silica model consists of a three-layer slab, with a

dehydroxylated surface and bottom oxygen atoms terminated

with H atoms (see Fig. 1a and b). Our strategy was to use this

‘‘healed plane of oxygen’’ to model a hydroxylated surface.

The resulting surface (obtained after reoptimization at 0 K of

the ‘‘Bernasconi slab’’) is shown in Fig. 1b. The atomic density

is 2.35 g cm�3. This density corresponds well to that reported

for real silica (2.2 g cm�3). The cell surface is 1.56 nm2. All Si

atoms have their complete coordination shell and all surface

Si atoms are hydroxylated and posses one or two SiOH

hydroxyl group (silanols). The SiOH density is 7.66 OH per

nm2. While this value is significantly higher than the generally

accepted silanol density for fumed silicas (4 to 5 per nm2), we

believe that it may be representative of precipitated silicas,

where SiOH densities between 7 and 8 per nm2 have been

reported;32 precipitated silicas are most probably relevant as

materials that may have been present in the prebiotic earth.

Also, the figure of 6.2 silanols per nm2 has been quoted for

biogenic silicas,33 indicating that these quite high silanol

density values are not unrealistic for silicas formed in

conditions of high water activity.

On silicas of lower OH density as commercial Degussa

Aerosil 380 which presents 5.1 silanols per nm2, these values

are average values taken over the whole surface and high

silanol density nano-zones on the surface are not unlikely to

exist. Indeed, experimental works on amorphous silica suggest

the coexistence of hydrophilic zones and hydrophobic ones,15

a hypothesis recently substantiated by a theoretical work.34

In the latter work, a silica surface of mean silanol density of

3.7 OH nm�2 is shown to exhibit zones free of silanols

coexisting with zones containing up to 7.5 silanols nm�2.

Also, the small size of the glycine molecule allows focusing

on a small proportion of the surface without formation of

chemical bonds with other surface groups. Finally, this high

density model is conserved because high silanol density zones,

with a known hydrophilic character, are the adsorption of

glycine, an amino acid of known hydrophilic character, or in

general a biofunction which contains few hydrophobic groups

on its interacting surface.

The repartition of the surface silanols in the model used is

5.1 geminal silanols (66%) per nm2, 2.5 terminal-associated

(44%). The silanol groups are H-bonded to each other or are

H-donating to a bridging O atom in a siloxane group. The

O–H bond lengths in the H bonds vary from 1.7 to 2.7 A.

Experimentally, the measured proportion of geminal silanols

depends on the type of silica and of the degree of humidity of

the atmosphere. Geminal silanols are expected to be stabilized

Table 1 Stabilization energies (from neutral glycine, NG) of the neutral (NG) and zwitterion (ZG) forms of glycine on vicinal silanols andgeminal silanol groups. Comparison with the stabilization energies of NGn, ZGn (G, n water molecules) complexes. Values in parenthesis indicatethe energies of G–water interaction calculated with B3LYP, 6-311++G** (kJ mol�1)

Terminal Geminal

NG ZGNG ZG

Conformer orientation Perp.a Para.b Perp.a Para.b Para.b Para.b

Number of H bonds with the surface 3 2 3 3 3 3(Estab/G)/kJ mol�1 �38 �98 Neutralisation �53 �133 �142NG/ZG water complexes NG2 NG3 NG4 ZG3 ZG4 ZG5(Estab/G)/kJ mol�1 �79 (�73) �121 (�122) �170 (�162) �96 (�100) �170 (�148) �198 (�181)a Perpendicular. b Parallel.


in the presence of water (vapor or liquid). Various authors

have reported that geminal silanols amount to a 9 to 30%

of the total silanol population on amorphous silica.35–37

A quite typical value of 14% geminal silanols was obtained

for an Aerosil-type silica by 29Si NMR.42 Again, these

percentages are average values and do not exclude surface

heterogeneity and the existence of particular zones

characterized by high geminal silanols density. The geminal

and terminal silanols all belong to a H-bond network where

each silanol forms one or two H bonds; the H bond length

varies between 1.87–1.99 A; the Si atoms bearing both silanols

are separated by about 3.00 A.

Finally, the silica tetrahedra are bonded to each other

forming rings. The model used here does not show any true

‘‘surface ring’’; however, the surface tetrahedral Si belongs to

rather large size rings (for example, several S12R rings), partly

at the surface and partly underneath the surface. This geome-

try ensures the flexibility of the surface atoms, as large size

rings impose lower constraints than small size ones. It can be

noted that very constrained rings (S2R, S3R) are also present

in this model, even though they are not located at the surface.

These constrained rings were created during the simulated

annealing MD at high temperature23 and are not present on a

real silica surface in the presence of water (either as a vapor or

liquid). Nevertheless, as those constrained rings are not

exposed at the surface, and belong to layers which are kept

frozen during the geometry optimization, they do not have any

influence on the surface reactivity of the slab.

The electrostatic potential of the surface was calculated in

order to compare the differences in acido/basicity between

terminal and geminal silanols (Fig. S1 in the ESI).w We

observe that geminal silanols are poorer in electrons than

vicinal ones. Knowing that the charge on the H atom of the

hydroxyl can be used to estimate its acidity as was done in a

former study,38 one can extrapolate this result and conclude

that geminal silanols have a more acidic character than

terminal ones, a result in agreement with previous theoretical

works.39,40 We can also note that one of the geminal silanols is

poly-H-bonded. Poly-H-bonded silanols have been reported to

exhibit an increased acidic character by comparison with

mono- and di-H-bonded silanols.41

B Interaction of water with the hydroxylated silica surface

Once the hydroxylated surface was established, a molecular

dynamics simulation in the presence of five water molecules

was performed. This procedure enabled us to gather

information on the most favorable conformations of the water

molecules adsorbed on the silanol groups, as well as a mean

value for the adsorption energy of molecular water on the

surface. The MD of the silica surface simulated a time of 2 to

8 ps at a temperature of 300 K.

Different starting configurations were built, in which the five

molecules were evenly spread on the whole silica surface

(Fig. 2a and additional results in ESI);w during the MD run,

the water molecules diffuse on the surface; when the

equilibrium is reached, they are located in the zone at the

surface with the highest density of silanols (Fig. 2c and

additional examples in the ESI).w Each water molecule is

involved in 2–4 H-bonds with silanols/water. After geometry

optimization of the most stable structures, the configuration

shown in Fig. 2c was obtained. From this result, the mean

energy of adsorption of water on a silanol is �61 kJ mol�1.

This value is slightly higher than the one obtained recently

by some of us in studying the affinity of terminal and geminal

silanols for water (�46 and �50 kJ mol�1 respectively).40 This

result confirms that H-bonded silanols (either terminal or

geminal ones) have an increased affinity towards water, as

recently confirmed by a theoretical approach.34

C Interaction of glycine with the silica surface

In a preliminary study, we studied how glycine interacts with

terminal and geminal silanols. Our aim was to investigated

whether the silanols of the silica surface are able to stabilize the

zwitterionic form of glycine over the neutral one. Therefore,

the two forms of glycine, neutral (NG) and zwitterion (ZG)

were submitted to standard geometry optimizations in two

configurations (the (C–C–N) backbone being perpendicular or

Fig. 2 (a) Starting configuration of the MD run at 300 K for five

water molecules on the silica surface; (b) total electronic energy versus

time elapsed in the MD run for 5 water molecules on the silica surface

at 300 K; (c) the most stable water-surface conformation obtained by

means of MD run at 300 K and subsequent optimization at 0 K.


parallel to the surface), forming H bond interactions with

terminal and geminal silanol groups of the surface.

Glycine in interaction with terminal silanol groups in

parallel and perpendicular orientations is shown in Fig. 3a

and b, and the energies of interaction are reported in Table 1.

In the perpendicular orientation, the COO(H) group

forms three H bonds with silanol groups. Starting from the

zwitterion form a spontaneous proton transfer from the

ammonium function to the COO function was observed. In

the parallel orientation, the zwitterion can be stabilized

(Fig. 3c); it is, however, much less stable than the neutral

form (by 45 kJ mol�1). Only two H bonds are formed between

the COO(H) moiety and the surface silanol groups. We notice

that the NH3+ moiety does not form any bond with silanols.

These calculations show that terminal silanol groups cannot

‘‘solvate’’ the glycine molecule (i.e. stabilize the ZG form over

the NG one), a trend in agreement with previous calculations

on silanol groups9,11,12 (indeed, we showed that four silanols

would be necessary to ‘‘solvate’’ glycine) and experimental

data.10,11 It is interesting to note that in this configuration, the

NH3+ function did not form any H bond with the surface

silanols; this rather low affinity of NH3+ towards silanols may

be explained by the acidic character of both the silanols and

the ammonium moiety.

The interaction of glycine with geminal silanols (through the

COO(H) function) was then investigated in the parallel

orientation (see Fig. 3d for the ZG conformer). The energy

of interaction is higher than when glycine interacts with

terminal silanol groups, suggesting that geminal silanols are

more acidic than terminal ones (the COO� moiety being a

base), a trend in agreement with our own computational

results40 and IR experimental data.42 In this configuration,

the zwitterion form is slightly more stable than the neutral

form. Again, no H-bond between the ammonium and the

silanols is formed.

With the increasing adsorption energy, the ZG form is

stabilized over the NG form, a trend evidenced in the case

of glycine microsolvated by water molecules25 and silanols.12

More precisely, the interaction energy of NG with the terminal

silanol groups, �98 kJ mol�1, is lower in absolute value than

the NG to ZG transition threshold calculated for G–water

complexes (�170 kJ mol�1) (see Table 1), explaining why the

NG form remains stabilized over the ZG form. In contrast,

considering the interaction with the geminal silanols, the

NG and ZG forms are both stabilized with �130 and

�140 kJ mol�1, respectively, thus slightly lowering the value

of the NG–ZG transition threshold. This can be due to the

attractive field generated by the silica surface, (see Fig. S1 in

the ESI).wAb initio MD runs were then performed to investigate the

possible modes of adsorption of glycine onto the hydroxylated

surface. In the starting configuration, the glycine in the ZG form

was put in interaction with either two vicinal terminal silanols

(Fig. 4a) or a geminal pair (Fig. 4b). In the first case, the ZG

conformer is unstable and a proton transfer occurs to form the

neutral glycine, a trend in agreement with results exposed in the

preceeding paragraph; then, the NG molecule detaches from the

terminal silanols to bridge one terminal and one geminal silanol,

and the NH2 moiety makes H bonds with silanols; simulta-

neously, the total energy slightly decreases (by around 0.5 eV),

indicating a stabilization (Fig. 4c and d). In contrast, the ZG

conformer bonded in the starting configuration to a geminal pair

through the COO function conserves the ZG form (again, in

agreement with the results obtained in the preceding paragraph)

Fig. 3 Optimized geometries obtained for the neutral (NG) or zwitterionic glycine (ZG) on (a)–(c) vicinal silanol groups: (a) NG parallel to the

surface, (b) NG perpendicular to the surface, (c) ZG parallel to the surface, (d) ZG on geminal silanol groups, parallel to the surface.


and evolves to stabilize andmake bonds between the COOmoiety

and one silanol of the geminal pair and one terminal silanol, and

additional H bonds from the ammonium to the silanols (Fig. 4e).

Proton exchanges between one geminal silanol and the COO

function were also observed. Finally, both MD runs indicate that

a global minimum in the potential surface is achieved when

glycine bridges one geminal and one terminal silanol, and the

ammonium group binds H bonds with silanols.

The configurations found at the local minima were then

submitted to a standard geometry optimization (Fig. 5 and

ESI)w and we indeed confirmed that glycine in the ZG con-

former bridging two silanols, one terminal and one geminal, is

the most stable configuration. It is interesting to note that this

time, the neutral form was not stable and a proton transfer from

the COO(H) group to the amine one spontaneously occurred

during the geometry optimization (thus requiring no activation

energy), with a gain of energy of 0.37 eV. In the final ZG

configuration, the OCO moiety is an H-bond acceptor from

three silanols and the NH3+ function is H bond donor to one

silanol. Other conformers are less stable: the cationic conformer

and the neutral form are 0.1 and 0.3 eV less stable respectively;

the optimized configurations are reported in the ESI.w

D Interaction of microsolvated glycine with the silica surface

In order to gradually bridge the gap between the gas/solid and

the liquid/solid interfaces, we have introduced solvent

molecules in the calculations; here, we consider microsolvated

glycine in interaction with a silica surface. It has been shown

theoretically and experimentally that five water molecules are

enough to microsolvate glycine ref. 25. We have thus

considered the ZG5 complex (zwitterionic glycine micro-

solvated with five water molecules) in interaction with the

silica surface. In a first step, MD runs were performed in order

to explore the configurations of glycine and water on the silica

surface. At 300 K, two starting configurations were considered

where the glycine molecule interacts through water molecules

with the silica surface, in a perpendicular and parallel mode. In

both cases, during the MD, after some hundreds of femto-

seconds, we observed the direct interaction of glycine through

COO� with a silanol group whereas the NH3+ moiety kept its

interaction with water molecules (Fig. 6). This confirms the

weak affinity between NH3+ and the acidic silanols. Starting

from the perpendicular orientation, the glycine molecule binds

a direct bond with a silanol group, then bends parallel to the

surface, in a conformation similar to that obtained with the

parallel mode (Fig. 6). The perpendicular to parallel transition

is accompanied by a decrease in energy, showing that glycine is

more stable in the parallel orientation to the surface. A MD

run was also performed at 400 K for the perpendicular

orientation; we observed the desorption of water molecules

and glycine from the surface and the neutralization of the

glycine molecule.

E Thermodesorption

Based on the present results, the desorption temperature of water

and glycine adsorbed on the different sites of the silica surface

was calculated. Indeed, the temperature of desorption at a given

partial pressure of water (glycine) in the gas phase is directly

related to the energy of adsorption of water (glycine) on the

Fig. 4 MD runs of glycine on the hydroxylated silica surface: (a)–(b)

starting configurations of glycine in interaction with (a) terminal

silanols, (b) geminal silanols; (c) total electronic energy versus time

elapsed in the MD runs at 300 K. Dashed line: glycine on terminal

silanols in the starting configuration. Solid line: glycine on geminal

silanols in the starting configuration. (d) and (e) Local minima obtained

in the case of (d) glycine on terminal silanols in the starting configura-

tion, and (e) glycine on geminal silanols in the starting configuration.

Fig. 5 Most stable configuration (Eads = �169.9 kJ mol�1) obtained

after geometry optimization at 0 K of glycine on the hydroxylated

silica surface. The glycine is in the ZG conformer, bridging one silanol

from a geminal pair and one terminal silanol. Three H bonds are

formed between COO and silanols, and one between the NH3+

function and a silanol.


surface. We first checked if water strongly coadsorbs with glycine

on the silica surface: therefore, starting from the ZG5 complex on

the surface, we removed the water molecules, and after optimiza-

tion, we calculated that the mean energy for desorption of water

to be equal to 70 kJ mol�1, a value near that of water adsorption

on silica (�61 kJ mol�1). So, we can consider that adsorption of

glycine and water are independent. Fig. 7 shows the different

stabilities of the species on the hydroxylated silica surface. Four

zones appear, depending on the temperature range: at the lowest

temperatures (To 325 K), glycine on silanols (either terminal or

geminal ones) and water are adsorbed on the silica surface; in the

second zone, (325–375 K), glycine is more stable in the gas phase

than on terminal silanols, so glycine is adsorbed only on geminal

sites; in the third zone (375–425 K), water is more stable in the

gas phase: in this domain, only glycine on geminal silanols is

adsorbed on the surface; finally, in the fourth zone, correspond-

ing to temperatures above 425 K, water and glycine have

desorbed from the surface. This result suggests that in the

RT-400 K range, there is coexistence of glycine in the gas phase,

glycine adsorbed on the silica surface and water coadsorbed with

glycine on the surface. This result is a prerequisite for the reaction

glycine (gas) + glycine (ads) to the peptide bond as studied by

Rimola et al.8,43

Discussion

The adsorption of glycine on silica was already studied using a

periodic approach by Rimola et al.9 using a crystalline silica

surface model. In this surface, the OH density was much lower

(2.2 OH nm�2) than in our model. Such a low OH density with

OH groups distant of 7 A corresponds to isolated silanols. As

stated by the authors, such a low OH coverage corresponds to

silica dehydrated at high temperature (800 K). Extending on

this interesting result on a system of very low water activity,

our approach gives a new information about the reactivity of a

fully hydroxylated silica, with the addition of discrete water

molecules on the surface, as our aim is to understand the

interplay between the solid, the AA and the water solvent in

the mechanisms of adsorption/reaction. We could thus extend

the study to a surface presenting ‘‘nest of hydroxyls’’, of local

silanol density of 7.7 silanol nm�2. It will certainly be inter-

esting to compare results obtained on this surface with alter-

native silica models having a intermediate silanols density,

such as the one we have recently developed, with silanol

density of 5.8 silanols nm�2.40

Rimola et al.9 showed that glycine at a low coverage

interacts only weakly with the surface isolated silanols (the

calculated heat of reaction was 56.9 kJ mol�1), which do not

act as a ‘‘solid solvent’’, a result in agreement with our own

calculations using minimal clusters.11,12 The present results

show that associated terminal silanols do not solvate glycine,

even if the heat of adsorption of glycine is slightly higher than

in the case studied by Rimola et al. (�98 kJ mol�1).

This higher interaction energy is likely due to the associated

character of the terminal silanols in the present study.

In addition, we could also study a new active site, namely

the associated geminal silanols: we found that associated

geminal silanols are more acidic than associated terminal ones,

which explains the more exothermic interaction of the glycine

carboxylate function with the geminal silanols.

The calculated energy of adsorption of glycine on geminal

silanols, �140 kJ mol�1 corresponds to the formation of three

H-bonds, thus to a mean energy of 46 kJ mol�1 per H-bond, a

Fig. 7 Surface energies (J m�2) as a function the temperature (K) of

the hydroxylated silica surface, without adsorbate (black line), with

5 water molecules (blue curve), with glycine adsorbed on vicinal

(green) and geminal (pink) silanols. Four zones are evidenced; they

are described in the text.

Fig. 6 MD runs for ZG5 on the silica surface at 300 K. Starting

configurations: (a) parallel orientation, (b) perpendicular orientation.

(c) Energy versus time (fs), blue: perpendicular orientation, pink:

parallel orientation. (d) Conformation obtained after standard

geometry optimization of the local minima in the MD run.


rather high value (the mean value of H bonds between water

molecules in several water clusters was evaluated as

23 kJ mol�1). Again, as observed for water, this higher energy

of interaction may be attributed to the associated character of

the geminal silanols and to cooperative hydrogen bindings.

The displacement of the water molecules to allow a direct

interaction of glycine (as found through the MD runs) with a

silanol group is also in agreement with this higher energy of

adsorption calculated for glycine as compared to water on

hydroxylated silica. This result may seem rather counter-

intuitive, as H bonds are expected to be weak bonds. However,

there is experimental evidence that glycine is strongly adsorbed

onto the silica surface through a H-bond network.10,11

The results presented here support our previous works

performed at the B3LYP level on small clusters: indeed, the

interaction energy of glycine with free silanols was calculated

at �110 kJ mol�1: it was found that those free silanols do not

solvate glycine and that water acts as a ZG co-stabilizing

agent. Using a periodic approach, an interaction energy of

�98 kJ mol�1 for neutral glycine on terminal silanols was

obtained. This value is in good agreement with that found

using small clusters and B3LYP approach.

The relaxation energy of the surface in the presence of glycine

was calculated to be equal to DErelax = �12 kJ mol�1.44 This

rather low energy of surface rearrangement is in agreement with

the expected flexibility of amorphous silica, and shows that even

within the periodic scheme, the size of the cell was big enough to

ensure a low energetic cost surface reconstruction.

Rimola et al.9 reported that the COO(H) function does not

bind to a unique SiOH, but bridges two silanols, despite their

rather long distance. Their result is in agreement with our

findings using clusters to mimic the silanols on silica.11 Our

present results are in line with this trend, as neither 0 K

calculations nor MD studies report the binding with one single

silanol as a local minimum. Such a result is also found when

studying the adsorption of glycine on an a-alumina surface:

multi-site adsorption on hydroxyls is favored over adsorption

on one single site.7 As a consequence, the glycine molecule lies

parallel to the surface (silica or alumina). We also showed here

that the presence of additional water molecules does not

change the orientation of glycine, parallel to the surface.

Moreover, glycine interacts preferentially through the carboxy-

late function directly with the silanol groups rather than

through water molecules. This suggests that glycine is able to

displace water molecules on the surface to form a bond

between the carboxylate function and the silanols. In contrast,

the ammonium does not exhibit the ability to substitute water

molecules on the surface. This is understandable when one

considers that silanol groups are acidic in nature, and that they

mostly interact with the basic carboxylate group than the acidic

ammonium. Interestingly, a similar trend was also found in the

case of glycine adsorption on a-alumina: even on m1-OH

groups, which have been characterized as rather basic groups,45

the ammonium group does not form H bonds, whereas the

carboxylate function makes H bonds with one or two

hydroxyls.7 Thus, it seems to be a general trend that there is

no perpendicular binding of glycine, but rather a parallel

adsorption mode where the carboxylate function interacts with

several hydroxyls, on the one hand, and the ammonium group

may also build H bonds with the surface. Our present

calculations show that the presence of water does not change

this tendency.

Conclusion

The interaction of glycine with an amorphous hydrophilic

silica surface, containing a high density of associated terminal

and geminal silanols, was investigated by means of periodic

DFT. It was found that the heat of interaction of glycine with

geminal silanols is higher than with terminal silanols. The

comparison with previous data suggests that the associated

silanols (either terminal or geminal) have an increased affinity

towards glycine than isolated ones. At room temperature,

glycine was predicted to bind to geminal groups through the

carboxylate function, lying parallel to the surface. Micro-

solvated glycine binds to the surface via its COO� function

rather than through water molecules. Through the combina-

tion of H bonds formation, the energy of adsorption is high

enough to ensure thermal stability until 400 K.

Finally it was shown that the presence of silanols of different

reactivities allows the coexistence of glycine grafted at the

surface and gaseous glycine in the gas phase.

Acknowledgements

The authors thank Prof. C. F. Bernasconi for kindly supplying

his amorphous silica model. The computation facilities

provided by national computational center IDRIS and by

CCRE (Universite Pierre et Marie Curie) are acknowledged.

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DFT study of the adsorption of microsolvated glycine on a hydrophilic amorphous silica surface

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