Effect of Amorphous AmmoniaâWater Ice onto Adsorption of Glycine

Article pubs.acs.org/JPCC

Effect of Amorphous Ammonia−Water Ice onto Adsorption of Glycine on Cometary Dust Grain and IR Spectroscopy Elizabeth Escamilla-Roa*,†,‡ and C. Ignacio Sainz-Díaz‡ †

Instituto de Astrofísica de Andalucía (CSIC), Glorieta de la Astronomía s/n, 18008 Granada, Spain Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Av. de las Palmeras 4, 18100 Granada, Spain

‡

ABSTRACT: The extraterrestrial origin of glycine has become a topic of great interest for astrobiology and it has been detected bonded to mineral surfaces in the dust of comet 81P/Wild 2 by the Stardust mission. The interactions of organic molecules with the dust grain surfaces shed light on possible routes for life from extraterrestrial space to Earth. The NH3 is one of the volatile components of cometary and interstellar ices. In this work we propose models that describe this scenario that consist of a quaternary system of one glycine molecule, a mixture of amorphous ammonia−water ice, and forsterite (100) surfaces (dipolar and nondipolar). Our quantum mechanical calculations show that the presence of amorphous ammonia/water ice increases the adsorption energy of glycine on the forsterite surface with respect to only amorphous water ice. In addition, we calculated the infrared (IR) frequencies to characterize the most reactive sites in the chemisorption processes with the mineral surface.

1. INTRODUCTION Comets are the most primitive bodies of the Solar System and generally believed to played a major role in bringing organic matter to the early Earth, enabling the prebiotic synthesis of biochemical compounds. The extraterrestrial origin of glycine, the simplest amino acid, has become a topic of great importance in astrobiology due to its unambiguous detection in the dust of comet 81P/Wild 2 by the Stardust mission. The glycine in this comet has an extraterrestrial carbon isotope signature, indicating that it was formed in space. The results indicated the presence of both free and bonded glycine in the comet. Elsila et al. (2009) proposed that the amine group (−NH2) of glycine may be covalently bonded to some surfaces.1 This discovery has great significance in the hypothesis about the origin of Life on Earth, proposing that the amino acids contained in grains of dust might be deposited on the surface of young planets following comet and asteroid impacts, making viable the extraterrestrial hypothesis of the origin of life proposed by Arrhenius. On Earth, glycine has been found in the carbonaceous chondrites of several meteorites, such as Murchison and Tagish Lake.2,3 However, glycine has not been detected spectroscopically in comets from the ground or with space-borne instrumentation yet.2,4 The dust particles in comets are composed of a heterogeneous mixture of amorphous and crystalline silicates, organic material, and other minor constituents such as iron sulfides and oxides. The presence of minerals in space may be of great importance in prebiotic synthesis.5 Olivine is the most abundant mineral that constitutes the dust grains and has been detected spectroscopically showing up as prominent emission bands in the mid-infrared.6 Olivine is a silicate that forms a complete solid solution between two end-members: forsterite (Mg-rich olivine) and fayalite (Fe-rich olivine). These dust © 2014 American Chemical Society

grains are embedded in a matrix of various ices, such as H2O, CO, CO2, NH3, and CH4.7 The ammonia molecule was the first polyatomic molecule detected in space8 and may be an important repository of nitrogen in interstellar and cometary dust.9 This molecule was detected in the nuclei of comets and can represent about a 1% level relative to water ice,10 although its content can be enhanced by taking into account the interior of ice bodies.11 The heterogeneous morphology of amorphous ices of water mixed with other components enhances their interaction with dust and organic12 molecules. Prebiotic synthesis of several organic molecules to produce glycine in the Interstellar Medium (ISM) has been studied in the gas phase from the theoretical and experimental sides.13−17 Experimental studies on spectroscopy of amorphous ices and ammonia−water ices have attracted great astrophysical interest.18−24 In addition, the mineral surface can catalyze the polymerization of organic molecules in the prebiotic synthesis.5 This interaction can be studied through the solid−gas interphase. Interactions on the mineral surface of organic molecules and amorphous ice components in comets and other extraterrestrial bodies can help to understand the origin and early evolution of life on Earth. The purpose of this work is to explore the effect of ammonia molecules on the adsorption processes of neutral glycine on the cometary grain surface. We previously studied the glycine− mineral surface interaction in two models: with and without amorphous water ice. In these models we found that the chemisorption process is produced in the interphase solid−gas of cometary dust.25,26 In this work, we improve on our previous Received: July 29, 2014 Revised: October 16, 2014 Published: October 16, 2014 26080

dx.doi.org/10.1021/jp507650w | J. Phys. Chem. C 2014, 118, 26080−26090

The Journal of Physical Chemistry C

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the slab, three upper SiO4 planes were optimized and the rest of the planes remained fixed. On the other hand, for the weak interactions we applied the semiempirical Grimme dispersion correction31 by fully optimizing the adsorption complex and reactant with the GGA/PBE/G06 method.32 This correction was applied only in a physisorbed complex for comparison.

model by adding ammonia molecules on amorphous water ice as a fundamental component of the mixture, to simulate a more realistic environment. In order to describe the interactions of glycine, amorphous dirty ice (ammonia−water), and cometary dust, we use quantum mechanical calculations.

2. METHODOLOGY We determined the geometric parameters and energies of the bulk and clean surfaces of forsterite and adsorption complexes by using first-principles calculations on periodical crystal structures based on density functional theory (DFT) with the generalized gradient approximation (GGA) and the PBE exchange correlation functional.27 We used the Dmol3 program, implemented in the Materials Studio (MS) package, including periodical boundary conditions.28 The electronic calculations were made with a DNP basis set (double-ζ augmented with polarization functions). The orbital cutoff quality was determined with a 0.1 eV atom−1 of energy accuracy threshold. We used semicore pseudopotentials (DSPP). The convergence criterion for the self-consistent field was 1 × 10−6. The optimization of geometries of different structures has been performed at 0 K. This methodology has been previously used successfully to describe similar adsorption processes.25,26 The harmonic vibrational frequencies were calculated by diagonalizing the mass-weighted second-derivative Hessian matrix generated by finite atomic displacements. In the adsorption processes, the geometry of the adsorbate (glycine, ammonia, and water molecules) was optimized alone at constant volume within a large periodical box with the same size of the adsorption complex. This adsorbate was also optimized with the periodical surface of the mineral at constant volume with the same crystal cell parameters. The surface energy per area unit (γ) was calculated as a measure of the thermodynamic stability of the surfaces as follows.29,30 γ=

Eclean surface − E bulk A

3. RESULTS AND DISCUSSION a. Mineral Surface and Models. Our models are based on the optimized crystal structure of forsterite which consists of independent SiO4 tetrahedra linked by divalent Mg cations with octahedral coordination. This mineral has an orthorhombic structure in the Pbnm space group with the crystallographic parameters of a = 4.756, b = 10.207, c = 5.980 Å with γ = β = α = 90°.33 There are several experimental and theoretical studies on hydration and stability of different surface faces.34−37 There is evidence of the (100) surface being reactive for water adsorption.36,38 On the other hand, theoretical models have demonstrated that the Mg atoms with low coordination in surfaces of steps, terrace, and corners are associated with high reactivity for adsorption process.39,40 Our optimized bulk yields crystal parameters that are very close to the experimental values33 with slight deviation of 1.17%, 1.57%, and 1.36% for a, b, and c, respectively.25 We increased the cell to obtain the 1 × 2 × 1 supercell of forsterite. The (100) surface was created by cleaving parallel to the a axis of the optimized bulk crystal lattice, After this cleavage, the crystal was enlarged along the perpendicular direction with respect to the surface, creating a vacuum spacing of 20.0 Å. The exploration of different terminations of this surface and the effect of defects in the crystal structure are very interesting but are out of the scope of this work. In our previous work we reported the geometrical parameters for the surface stacking sequences which produce two surfaces: dipolar and nondipolar terminations of the (100) surface. According to previous theoretical works,34 these surfaces should remain intact tetrahedra with a surface area 125.44 Å2. In both surfaces the slab generated contains five SiO4 horizontal planes with alternate Mg atoms. The (100) surfaces were optimized for a relaxed slab of the upper three SiO4 planes, and the rest of the planes were fixed, yielding a relaxed slab of the surface. The surface energies were 2.27 and 2.59 J/m2, for dipolar and nondipolar surfaces, respectively. These values are in good agreement with the previous theoretical values of 2.25 and 2.57 J/m2 reported for Watson et al. (1997) and de Leeuw et al. (2000). The slab of the dipolar surface has several undercoordinated Mg atoms in the exposed surface (Figure 1a): 4fold (4f), 3-fold (3f), and 2-fold (2f). In the nondipolar relaxed surface, the Mg atoms have different coordination (Figure 1b): 4-fold (4f), (4f*) 3-fold (3f), and 5-fold (5f). The 4f* indicates a Mg (4f) atom on a top side on the surface. For both surfaces, the geometrical parameters of Mg−O and Si−O distances are in good agreement with previous results.30,34 We studied previously the effect of amorphous water ice in the adsorption of glycine, showing that water molecules increase the adsorption energy on mineral surfaces with respect to only neutral glycine.25,26 The ammonia molecule is a volatile compound of cometary dust. In this work we have simulated a more realistic scenario in which we include the effect of this molecule on adsorption glycine. Hence, we propose two models: (i) a model of a mixture of amorphous ammonia− water ice and one glycine molecule set to interact with the mineral surfaces; and (ii) a model by layers in which a thin layer

(1)

where γ is the surface energy. Eclean‑surface is the surface energy of the crystal, Ebulk is the energy of an equivalent number of bulk ions, and A is the surface area. Analogously, in the surface with adsorbate the surface energy γads will be γads =

Esurface+absorbate − E bulk − nEadsorbate A

(2)

where Esurface+adsorbate is the total energy of the relaxed surface with the adsorbate, and nEadsorbate is the energy of the n adsorbate molecules. To obtain the adsorption energy, we use the following equation: Exads /forst = − (Ex /forst(100) − Eforst(100) − nEadsorbate)

(3)

where Ex/forst(100), Eforst(100), and nEadsorbate are the total energies of the forsterite (100) surface with the X-chemical species (complex adsorbed) on the surface, the pristine forsterite surface, and the total electronic energies of the n chemical species involved, respectively. All chemical species were adsorbed on a 1 × 2 × 1 unit cell of (100) surfaces of forsterite (dipolar and nondipolar) as a model of olivine mineral, a component of dust grains. The optimization of these complexes was similar to that of the clean forsterite surface; in 26081



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Figure 1. Pristine forsterite (100) surface: dipolar (a) and nonpolar (b). O, Si, and Mg atoms are displayed as red, yellow, and green color, respectively. The Mg site with different coordination on surfaces is as follows: 4-fold (4f) and (4f*) on top-surface, 3-fold (3f), and 2-fold (2f).

of amorphous ammonia−water ice covers the forsterite surfaces (nondipolar) and one glycine molecule is adsorbed in a second adsorption process. b. Adsorption of a Mixture of Glycine and Amorphous Ammonia−Water Ice onto Surface Grain Cometary. We studied the effect of a mix of dirty amorphous ice in the ratio 3H2O + 1NH3, on the adsorption process of glycine onto cometary grain surfaces. All molecules (one of glycine, one of ammonia, and three of water per unit cell in a periodical surface) were placed simultaneously as a mixture, where all components were distributed randomly above both surfaces (dipolar and nondipolar) at an average distance of 3 Å. The glycine molecule was oriented parallel to the surface according to our previous studies.25 After a full optimization of both adsorption complexes, we found that the ammonia molecule is adsorbed in an associative process on both surfaces. This behavior is similar to the growth of amorphous ammonia− water ice on the forsterite surfaces without glycine.40 The water molecules are adsorbed through both associative and dissociative processes, generating hydroxylated and hydrated sites. This behavior was reported in previous adsorption processes of water molecule on this mineral surface.26,34,37 Besides, glycine is adsorbed through the carboxylic terminal group forming monodentate and monodentate binuclear adsorption complexes for dipolar and nondipolar surfaces, respectively. In our early work we found that glycine, in gas phase without ice, has a preference for perpendicular orientation to the surface. For dipolar surface (Figure 2a) the NH3 molecule interacts with the surface through the nitrogen atom forming an Mg−N coordination bond with a distance of 2.13 Å to the adsorption

Figure 2. Direct adsorption of amorphous ammonia−water ice and neutral glycine onto the dipolar surface. The stable complex D-fors/ 3H2O+NH3+gly in different projections (a and b). Intermediate complex (one water dissociated) on dipolar surface (c).

site on the surface that corresponds to a low coordination site of Mg (2f) on the pristine surface (Figure 1a). When this Mg atom interacts with the N atom, the coordination changes to 3f, due to the approach of a vicinal internal O atom and the NH3 adsorption. This ammonia molecule is stabilized by several H bondings of the H atoms with a vicinal OSi group on the surface (H···O distance of 2.07 Å), with the O atom of the topsurface SiOMg group (H···O distance of 2.59 Å) and with the O atom of one water molecule adsorbed (H···O distance of 2.02 Å). This last water molecule is solvating the ammonia molecule with a strong H bond, and at the same time it is interacting weakly with the mineral surface (water molecule in the extreme left-hand side of Figure 2a). The other two water molecules are adsorbed by an associative process where the O atoms are coordinated with the surface Mg cations with Mg−O distances of 1.99−2.06 Å. These water molecules are stabilized forming strong H bonds with one undercoordinated O atom of a OSi group with H···O distances of 1.44−1.80 Å (Figure 2b, 26082



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two water molecules on the right side). The surface changed during the adsorption process owing to the effect of the water molecules: One water molecule is adsorbed with the O atom joined on one Mg (3f) atom of the pristine (100) surface, increasing the coordination of this Mg to 4f and this Mg moved along the a axis approaching the vicinal O atoms (left side of Figure 2a compared with Figure 1a); and the other water molecule is joined to another Mg (4f) site. However, the coordination of this Mg cation does not change. During this last adsorption, the top-surface Mg−OSi bond is broken (back part of Figure 2a), the Mg recovers its 4f coordination with the water adsorbate, and the O atom of the OSi group remains undercoordinated. This undersaturation obliges the vicinal Mg (3f) atom of the (100) plane to move toward the Si atom, and its undersaturation is compensated with strong H bonds of both adsorbed water molecules. However, we found the existence of a dissociation of one water molecule in the pathway during the optimization process (Figure 2c). The highly reactive undercoordinated OSi group traps the H atom of the water molecule which is approaching the Mg 4f, dissociating this water molecule whose OH group joins to the Mg (right side of Figure 2a and left side of Figure 2c). Nevertheless, this water molecule is not completely dissociated, because the H atom is maintained at 1.316 Å to the OH group (Figure 2c). However, this structure is not stable, because the H atom of the new HOSi group goes back to the original water molecule coordinating the Mg (4f) during a further optimization process. On the other hand, glycine is chemisorbed through the carbonyl group forming the monodentate adsorption complex (D-fors/3H2O+NH3+gly), where one O atom of the carbonyl group is coordinated with a Mg (2f) site (Figure 2a). This adsorption modifies the coordination of this Mg to 3f with a Mg−Ogly bond distance of 2.04 Å. The H atom of the carboxylic group is in an anti conformation with respect to the carbonyl group and it is oriented toward the amino one with a N···H distance of 1.73 Å. The glycine molecule is twisted with one H atom of the amino group oriented to the surface O atoms forming a H bond with an NH···O distance of 2.1 Å (Figure 2c). Similar behavior has been observed previously on this surface with only amorphous water ice.25,26 In the case of the nondipolar surface, two water molecules are chemisorbed by the associative and dissociative modes, i.e., one molecule remains completely (center left side of Figure 3a) and the other water molecule is dissociated to form OH groups on mineral surface (back part of Figure 3a). The additional water molecule is physisorbed out of the surface (fors/3H2O +NH3+gly, top left side of Figure 3a). This adsorption process also changes the atomic arrangements on the surface, as a function of the adsorption Mg sites. One water molecule is adsorbed on the Mg (3f) site of the pristine surface forming a new 4-coordination (4f) (left-hand side of Figure 3a). The OH group of the dissociated water molecule is adsorbed simultaneously on two Mg (4f) sites of the pristine surface, forming a bridging MgOHMg group (Mg−OH bond distance of 2.0 Å). The OH has transformed the surface to give a new and higher coordination of one Mg (4f) atom to a 5f one. This last Mg site also acquires a coordination with glycine, but at the same time it loses the coordination with the vicinal SiO group, which is protonated with the H atom of the dissociated water molecule, forming a SiOHMg group with d(Mg−OH) = 1.99 Å and d(Si−OH) = 1.73 Å (left-hand side of Figure 3b). The ammonia molecule is adsorbed on the Mg (4f*) surface site

Figure 3. Stable complex onto nondipolar surface, fors-H2O fors/ 3H2O+NH3+gly, in different projections: unit cell view from the (110) plane (a) and view of a 1 × 2 × 1 cell (b).

with a coordinated Mg−N bond distance of 2.20 Å (right part of Figure 3a). This adsorption provokes the Mg site to lose the coordination with the vicinal SiO group (from a vicinal unit cell), and at the same time a new silanol group (SiOH) is created (central part of Figure 3b). All these geometrical parameters are consistent with previous experimental and theoretical results.25,26,40−43 The glycine molecule is adsorbed through a dissociative process with one O atom of the carboxylate group joined by two Mg 4f sites (fors/3H2O+NH3+gly) (Figure 3b). Following the IUPAC nomenclature for coordination bonding structures, we consider the number of surface cations joined to the adsorbate as the “nuclearity” of the absorption complex, and the number of bonds from the adsorbate to the surface as the “denticity” of the ligand in the adsorption complex, as mondentate, bidentate, and so forth.44 Hence in this case we can consider that the glycine adsorbate forms a monodentate binuclear adsorption complex. The other O carboxylic atom is not oriented to the surface and is not joined to any Mg surface cation. Nevertheless, this O atom is stabilized forming an H bond with an H atom of a MgOHMg group (O···H distance of 2.28 Å) formed during the previous adsorption steps (right part of Figure 3b). The proton dissociated from the carboxylic group is joined to a surface O atom forming a silanol group (SiOH) (central part of Figure 3b). A network of H bonding is formed among all adsorbates. The water chemisorbed associatively forms an H bond with the glycine amino group (N···H distance of 2.04 Å). The physisorbed water molecule is trapped with three H bonds: a strong H bond with the former water molecule (O···H distance of 1.56 Å); another strong H bond with a top surface SiO group 26083



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(O···H distance of 1.59 Å); and other weak H bond with the O atom of the carboxylate moiety (O···H distance of 2.27 Å) (Figure 3b). This bridging adsorption mode enhances the adsorption energy with respect to the monodentate−mononuclear mode that occurs in the dipolar surface. The adsorption energy is 46.15 kcal/mol higher in the nondipolar surface than in the dipolar one (Table 1), owing probably to the dissociative water Table 1. Adsorption Energy of Glycine (gly) Mixture with Amorphous Ice (NH3/H2O) Absorbed on the Dipolar (Dfors) and Nondipolar (fors) (100) Forsterite Surfaces adsorption complexesa

adsorption energy (kcal/mol)

D-fors/(5H2O+gly)b fors/(5H2O+gly)b D-fors/(3H2O+NH3+gly) fors/(3H2O+NH3+gly) fors-(6H2O+2NH3)/gly

129.15 157.91 151.50 197.65 19.66 (26.60)c

Figure 4. Intermediate complex (zwitterionic form) formed during the adsorption process of adsorbates onto nondipolar forsterite surface.

a

Surface/adsorbate, i.e., D-fors/(5H2O+gly) means adsorption of a mixture of amorphous water ice and glycine on mineral surface, and fors-(6H2O+2NH3)/gly means adsorption of one glycine on a mineral surface covered with (6H2O+2NH3). bPrevious work.26 cDFT calculations including dispersion correction.

5a) and a second water molecule is physisorbed forming a H bond with a top-surface O atom, d(O···H) = 1.73 Å. (ii) A third water molecule is adsorbed in an associative process in a Mg (4f) site forming a bridging binuclear complex MgOH2Mg (Figure 5b). In this step this water molecule forms a H bond with the glycine carbonyl group and a strong intramolecular H bond in glycine molecule is formed (N···HO distance of 1.31 Å). (iii) Dissociation of the carboxylic group to form the zwitterionic glycine, the H atom jumps to the amino group of glycine. This dissociation increases the interaction of the carbonyl group with the H atom of the bridging binuclear water adsorbed dissociating this water molecule. One H atom of this water is transferred to a Mg (4f*, top of the surface) site, forming a SiOHMg group (right side of Figure 5c). On the other hand, the previous chemisorbed water molecule has a strong hydrogen bond with a SiOMg on surface, d(HOH··· OSi) = 1.33 Å, and stabilizes the ammonium group with a H bonding, d(O···H) = 2.09 Å (Figure 5c). (iv) Adsorption in a monodentate mode of glycinate by the carboxylic group with one Mg cation and, at the same time, the chemisorbed water molecule (initially associated) is dissociated to produce silanol (SiOH) and MgOH groups of surface (Figure 5d) maintaining a H bonding network of d(SiOH··· OHMg) = 1.36 Å and d(MgHO···HNgly) = 1.97 Å. (v) Proton transfer of one ammonium H atom of glycine to one MgOH formed in the former step, regenerating one water molecule. At the same time, a new (O−Mg) bond is created between the carboxylate group and two Mg surface cations which formed an Mg−Ogly−Mg moiety. Hence, the glycine adsorbed forms a monodentate−binuclear adsorption complex with the mineral surface (Figure 5e). c. Effect of Surface Energy on the Adsorption Processes of the Mixture of Glycine with Dirty Amorphous Ice onto Grain Mineral Surface. In order to study the effect of adsorbed molecules onto the surface, we calculated the surface energy (γads) for the surface with adsorbates (eqs 2). The surface energy decreases more with respect to the clean surface when the adsorbate is adsorbed more strongly because of the stabilization of the surface. The γads with glycine and amorphous ammonia ice are 1.40 and 1.44 J/m2 for dipolar and nondipolar surface, respectively. These values are close each other and indicate that the adsorption process is strong, due to the high decrease of γads with respect

molecule and the strong chemisorption of glycine that breaks and forms new bonds on the mineral surface such as a transfer proton to the surface and the bridging adsorption mode. This behavior was also observed in the adsorption of glycine mixture with water amorphous ice onto the nondipolar surface26 and previous theoretical studies of the glycine adsorbed on Cr2O3 surface.42 On both surfaces the adsorption energy indicates that ammonia molecules enclosed in amorphous ice can increase the adsorption energy of glycine with respect to glycine mixed with only water ice.26 Observing the adsorption complexes, the glycine molecule has lost the acid H atom onto the nondipolar surface and this does not occur on the dipolar surface. In order to understand the formation of the H bonding network, we explored the sequence of sorption steps during the optimization process and we found an intermediate step before finishing the chemisorption process. In this intermediate the glycine adopts a zwitterionic form. This effect is due to the dipolar molecules that are present in the mixture of amorphous ice (water and ammonia) and produces intramolecular changes in the amino acid from a neutral form to a zwitterion. This process is very significant due to the intramolecular change in glycine produced by the presence of water, and this has been also observed experimentally.45 However, this intermediate is not stable enough and during the optimization the zwitterionic form is lost, obtaining a neutral form of glycine according to experimental works in which neutral form was detected.17 In the intermediate structure (with zwitterionic form), the glycine molecule interacts with the nondipolar surface in a perpendicular orientation with respect to the surface (Figure 4). The +NH3CH2COO− is formed when a proton is transferred from the −COOH to the −NH2 functional groups. In order to describe the intermediate process, we propose a schematic mechanism of reaction of water, glycine, and nondipolar surface, as follows: (i) A first step of the simultaneous chemisorption of water and ammonia molecules (associative process) adsorbed on the Mg (3f and 4f*) sites of pristine surface, respectively (Figure 26084



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Figure 5. Reaction path to produce the intermediate complex on intramolecular transfer of one H atom from carboxylic to amino group of glycine on non-dipolar surface, each step is described with two figures, up/down, that represent two orientations: views from the (010) (up) and (100) (down) planes: adsorption of NH3 and H2O (associated) (a), adsorption of a second H2O molecule in a bidentate mode (b), formation of NH3 group (zwitterionic form) and the H2O molecule (bidentate mode) is dissociated (c), the dissociation of previous H2O molecule adsorbed in an 26085



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Figure 5. continued associative process and adsorption of glycine molecule to monodentate mode (d), adsorption of glycine in a monodentate−binuclear mode (Mg−Ogly−Mg) and reassociation of one H2O molecule (e).

to the pristine surface (2.27 and 2.59 J/m2 for dipolar and nondipolar surface, respectively). Taking into account our previous study of γads of amorphous ammonia−water ice onto this surface, we compare the adsorption in a simultaneous associative process of water, glycine, and ammonia molecules with the coverage on this surface of ammonia molecules40 in an associative process. In this case, four Mg sites have reacted with molecules of the adsorbate mixture, i.e., two water, glycine (monodentate mode), and one ammonia molecule, yielding a γads of 1.4 J/m2. This value is close to that for the adsorption of only four molecules of NH3 (γads = 1.5 J/m2) obtained in this model. In the nondipolar surface the number of molecules directly adsorbed is the same (2H2O+glycine+NH3). However, the water molecules have been dissociated and glycine is adsorbed by a bridging mode transferring a proton toward the surface O atom. Taking into account that Mg sites have a relationship with the reaction process on the surface, the dissociative process increases the coverage of the reactive sites on the nondipolar surface, i.e., five Mg atoms have new coordination with H2O, OH, NH3, and 2Mg−Ogly (bridging mode), yielding a γads of 1.44 J/m2. This is significantly lower than with the coverage of only 5 ammonia molecules on nondipolar surface (γads of 1.98 J/m2), where only associative processes exist. Hence, this difference is due to the dissociative mode with higher adsorption energy where two H atoms have been adsorbed on SiO and MgOSi sites and the bridging monodentate−binuclear adsorption mode of glycinate increases the stability of this surface. In our previous work we saturated the Mg sites with seven NH3 molecules in associative mode; the adsorbed energy surface (γads) was 1.83 J/m2.40 As a result of this, the dissociative process stabilized the surface more than the associative process. Therefore, the adsorption energy and surface energy have a great relationship in the chemisorption process; this behavior is consistent with previous work.29,34,40,46−48 d. Adsorption of Glycine onto Coating Mineral Surface of Amorphous Ammonia−Water Ice. In order to understand the interaction of glycine with different environments of cometary dust, we continue with the analysis taking into account the “layer” model of the interaction of glycine molecule with an ice substrate on top of a nondipolar mineral surface. In our recent work we reported quantum mechanical calculations of models exploring the interactions of amorphous ammonia−water ice onto the forsterite surface, finding that ammonia has a similar affinity to the forsterite surface as water. Taking into account the astrophysical study of possible interaction modes of ice mantle (ammonia−water) with grain,49,50 we studied possible scenarios to grow amorphous ammonia−water ice in the solid−gas interphase. We found that a mixture of amorphous dirty ice (ammonia−water) and forsterite (100) surfaces (dipolar and nondipolar) can produce a stable amorphous ice.40 This model consists of a mixture of water and ammonia molecules with a ratio 6H2O + 2NH3 (Figure 6), that corresponds to a coverage of 6.38 molecules/ nm2 and energy surface of 1.33 J/m2. With this ratio most Mg sites are occupied by the adsorbates.

Figure 6. Adsorption complex of glycine onto nondipolar mineral surface covered with a thin layer of dirty amorphous ice (6H2O:2NH3), fors-6H2O+2NH3/gly.

Water molecules having associative and dissociative processes producing hydroxylated and hydrated sites, such that four water molecules are adsorbed at Mg sites, forming O−Mg bonds, and two water molecules are dissociated. In these dissociated molecules, the OH groups are joined to Mg (3f) surface sites forming MgOH groups and the H atoms are joined to the nearby Si cations forming SiOH groups, being consistent with previous experimental51 and theoretical works.26,37 One ammonia molecule is adsorbed directly to one Mg(4f) atom of the top-surface through the interaction of an electron lone-pair of the N atom with the Mg atom of the surface forming a coordinated Mg−N bond. The other ammonia molecule is trapped out of the mineral surface forming H bonds with the vicinal water molecules. The geometrical parameters were detailed in our recent work on amorphous ammonia− water ice.40 The next step is the adsorption of one neutral glycine molecule onto the mineral surface covered with amorphous dirty ammonia−water ice, placing it in a parallel configuration at 4 Å over the layer of dirty amorphous ice preadsorbed onto the nondipolar (100) forsterite surface. Our previous theoretical calculations indicated that parallel forms favored the adsorption process in this mineral.25 The adsorbed complex shows that glycine has H bonds with vicinal water molecules preadsorbed onto the surface through the NH2 group and the O atom of the OH terminal group of glycine (fors-6H2O+2NH3/gly) with average distances of 2 Å. The arrangement of the water molecules on the mineral surface did not change during the glycine adsorption (Figure 6). The adsorption energy of one glycine molecule shows that the interaction between the amino acid and the amorphous dirty ice-covered substrate is weak, resulting in a physisorption process (see Table 1). The adsorption energy is 19.66 kcal/ mol, being slightly higher than the adsorption of glycine on this surface of forsterite covered with clean water ice (18.57 kcal/ mol).26 This means that the adsorption of glycine is more favorable when the mineral surface is covered with dirty ammonia−water ice than with clean water ice. 26086



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Table 2. Vibration Frequencies (cm−1) of a Mixture of Glycine (gly) and Amorphous Dirty Ammonia Ice (3H2O:NH3) Adsorbed onto Dipolar and Nondipolar Surfaces, and Free Glycine Molecule (in Brackets) and Previous Data vibration modea

dipolar

nondipolar

υ(OH)(water joined with Mg 3f) υ(OH)(water physisorbed, free OH) υ(OH)(water joined with Mg 3f) δ(HOH) υ(MOH) δ(SiOH) υ(NH)as (NH3) υ(NH)s (NH3) δ(HNH)as (NH3) δ(HNH)s (NH3) δ (NH3)umbrella (NH3) υ(NH2)as (gly) υ(CH2)as (gly) υ(CH2)s (gly) δ(HCH) (gly) υ(OH) (gly) υ(CO) (gly) δ(HNH) (gly) δ(OH) (gly)

3767b, 3190c 3583b, 3366c 2984g, 1986g 1610c, 1588b, 1569c

3531d 3676b 2926g, 2613g 1708b, 1655c 3705i, 2973j, 2808k 1311j, 1261k 3559, 3509 3388 1638 1616 1191 3443b, 3036c 3017 2944 1448

3340m 3240m 1600m

1680 (1764) 1572 (1636)

1720e, 1690p 1630r

3446, 3322 3229 1655, 1626 1210 3525, 3309g (3512) 3029b, 2966c (3013) 1430 (1417) 2857 1696 1574 1455

previous 3696e

2930−3746f

1656e

1639−1688h 2738l, 2554h 1266h 3482f, 3523f 3445f 1645f, 1627f

1140m, 1225n 3355o 2943o 1428o, 1423e

1212f, 1186f 3535h, 3501h 3035h 2934h 1418h,l, 1441h 2738l 1674q, 1441h 1618l, 1567h

a

Asymmetric (as) and symmetric (s). bGroup with low interaction with surface. cGroup oriented toward surface. dGroup oriented to the amino group of glycine. ePrevious experimental values.21 fPrevious theoretical values from Escamilla-Roa et al.40 gGroup oriented to a top-surface O−Si group, forming strong H bonds. hCalculated values from Escamilla-Roa et al.25,26 iMgOHMg group. jSiOHMg group forming a H bond. kAlone SiOH group. lCalculated values from Rimola et al.56 mExperimental values of ammonia adsorbed on Pt surface from Sexton et al.23 nExperimental values of ammonia adsorbed on TiO2 surface.24 oExperimental values of alkaline glycine salts.22 pExperimental values of carboxylic acids on silicate surface.58 qExperimental values of acetate adsorbed on rutile.57 rExperimental values of glycine adsorbed on silica.41

molecule (3767 cm−1). Within this ν(OH) range, the frequencies of the rest of OH groups will appear depending on the strength of local interactions. For example, the another OH group of the last chemisorbed water molecule shows a lower frequency (3190 cm−1) because it is oriented toward to surface and the H atoms have some interactions with the surface O atoms. A similar effect was observed in the physisorbed water molecule, where the OH group oriented to the surface has a lower frequency (3366 cm−1) than the OH without these interactions (3583 cm−1). A special OH group forms an extremely strong H bond, d(H···O) = 1.44 Å, and its ν(OH) band appears at 1986 cm−1. With respect to the ammonia molecule, the stretching mode υ(NH)as of the NH bond nonoriented to the surface appears at 3446 cm−1. However, the another NH bond has a υ(NH)as band at lower frequency (3322 cm−1) due to the H bond between this H atom and the vicinal O−Si group. These values are consistent with previous experimental23,24 and theoretical studies of adsorbed ammonia on mineral surfaces.40 We observed that the asymmetric and umbrella bending mode frequencies of the adsorbed ammonia group are close to the values of our recent work of the amorphous ice (3H2O:1NH3) adsorbed on this surface.40 The glycine molecule mixed with amorphous ice (3H2O:1NH3) and adsorbed on the surface shows two υ(NH) bands at 3525 cm−1 (for the NH nonoriented to the surface) and 3309 cm−1 (for the NH forming a H bond with a surface O atom). Again, this weak interaction of the N−H bond decreases the bond energy and then the υ(NH) frequency. On the other hand, the H−C−H stretching (υ) and H−C−H bending (δ) bands are close to the previous one detected on the model of the glycine mixture with amorphous water ice adsorbed onto surface,26 and previous experimental and

On the other hand, we reoptimized this adsorption complex, with PBE/GGA/G06 calculation including the semiempirical Grimme correction for dispersion interactions (DFT-D).31 The adsorption energy (DFT-D) was slightly higher than without this correction (26.60 kcal/mol). This means that this Grimme dispersion correction overestimates the weak interactions in our system, probably due to the coexistence of H bonds, according to previous works indicating that this correction cannot describe both weak and H bonding interactions in similar systems.52−54 e. Spectroscopic Properties of the Adsorption of Glycine and Amorphous Ammonia−Water Ice onto a (100) Forsterite Surface. We calculated the main vibrational frequencies of the chemisorbed structures for adsorption of glycine mixture with dirty ammonia ice (3H2O:1NH3) onto a mineral surface (dipolar and nondipolar). In Table 2 we summarize these frequencies along with values of previous experimental and theoretical works related to this model. In the dipolar surface, the stretching ν(OH) mode frequencies, corresponding to the water chemisorbed on the surface, appear at the range of 2984−3767 cm−1 and the δ(HOH) bands are found at 1588−1610 cm−1. These values are within the range of our previous result of adsorption of amorphous water and ammonia−water ice on this surface.26,40 The high value of ν(OH) at 3767 cm−1 is due to the high coordination of this chemisorbed water molecule with the Mg being consistent with values observed in brucite.55 These frequencies are very sensitive to the local environment interactions. For example, the water molecule chemisorbed on the surface Mg (3f) has a OH group with a strong H bond with the vicinal OSi group; hence, its ν(OH) vibration will appear at lower frequency, 2984 cm−1, than the OH group oriented out of the surface of another chemisorbed water 26087



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theoretical frequencies for δ(HCH) found at 1423 and 1418 cm−1, respectively.26,56,57 Another peculiar frequency is detected for the υ(OH) mode of glycine at low frequency, 2857 cm−1, due to the strong intramolecular H bondings according to previous studies.56 In the nondipolar surface, the adsorbed complex has a similar effect on the H bonding interactions and the υ(OH) frequencies observed. In the water molecule chemisorbed on the Mg (3f), the OH bond oriented to the amino group of glycine shows a lower υ(OH) frequency (3531 cm−1) than that of the OH bond nonoriented to the surface (3676 cm−1). This frequency shift is smaller than on the dipolar surface because the interaction is weaker. The hydroxylated surface groups show different υ(OH) frequencies depending on the nature of the cations joined to the OH group. The υ(OH) bands at 3705 and 2973 cm−1 are assigned to the MgOHMg and SiOHMg bridging groups, respectively. The ν(SiO−H) mode appears at 2808 cm−1 being consistent with previous calculations of glycine adsorption on silica surface (2738 cm−1).56 However, in our previous work, this band appeared at lower frequency owing to the strong hydrogen bonding with the neighbor functional groups that do not occur in the present work. On the other hand, the δ(SiOH) bands appear at 1311 and 1261 cm−1 corresponding to the SiOHMg and SiOH groups, respectively. On the nondipolar surface, the NH3 chemisorbed shows that υ(NH2)as and υ(NH2)s modes appear at higher frequency than in the dipolar surface, due to the lack of strong interactions with the vicinal groups. Nevertheless, two υ(NH2)as bands are detected, where the band that appears at lower frequency (3509 cm−1) corresponds to the NH bond oriented to the surface. On the other hand the δ(NH3)umbrella band appears at similar frequency to the dipolar surface, indicating that on both surfaces the ammonia groups are adsorbed in the same way. The glycine molecule was chemiadsorbed only by the carboxylate group with one O atom coordinated to two Mg surface cations in a monodentate−binuclear mode. This fact produces a frequency shift in the υ(CO) vibration mode appearing at 1680 cm−1, whereas this band appears at 1764 cm−1 in the free glycine molecule. This is consistent with previous experimental values of carboxylic acids adsorbed on silica58 and rutile57 surfaces. However, this frequency is 238 cm−1 higher than in our previous study of adsorption of glycine without ammonia.25 This difference can be due to the Mg−Ogly coordination forming different adsorption modes according to previous works.57 Nevertheless, this value is in good agreement with the experimental range reported for adsorption of acetate and glycine on several surfaces.21,57,58 On the other hand, we have found that stretching and bending modes of the CH2 group of adsorbed glycine are close to the value of the glycine mixture with amorphous water ice adsorbed on this surface.26 Also, this value is close to experimental values of glycine adsorbed on rutile surfaces.22 In the amino group we detect two υ(NH2)as frequency values at 3443 and 3036 cm−1. The band at lower frequency corresponds to the N−H bond oriented to the surface O atoms, d(NH2··· Osurface) = 1.7 Å, and these interactions decrease the υ(NH2)as frequency.

ammonia−water ice in the adsorption process of glycine onto two mineral surfaces (dipolar and nondipolar) of forsterite. We propose two models to simulate the interaction of adsorbates with the surface of dust mineral (simultaneous and layered adsorption). In the first model of simultaneous adsorption of disordered molecules of water, ammonia, and neutral glycine deposited on the mineral surface, the adsorption of the mixture is through a chemisorptions process on both kinds of surface. Water molecules are chemisorbed through the associative process on the dipolar surface. However, on the nondipolar surface water molecules are chemisorbed by dissociative and associative processes. This behavior was also observed in our previous studies of adsorption of amorphous water ice, in which only the nondipolar surface of forsterite can produce dissociated water. On both surfaces ammonia molecules are adsorbed only in associative processes, i.e., the NH3 molecules remain entirely, forming a Mg−N bond. The amino acid molecule chemisorbed through its carboxylic group that interacts on the most reactive site on the surface, i.e., at unsaturated Mg2+ sites. Glycine molecule adsorbed in a monodentate−mononuclear mode on the dipolar surface and a monodentate−binuclear mode on the nondipolar surface. The adsorption energy indicates that glycine has a preference to the nondipolar surface, probably due to the bridging binuclear adsorption mode that increases the stability. The bridging mode is favored energetically; this result also resembles glycine in our previous work and is in good agreement with other work on glycine and organic molecules adsorbed onto oxides. It is important to remark that on the nondipolar surface we found an intermediate and a mechanism of the adsorption process where neutral glycine changes its zwitterionic form. The adsorption mechanism involves the intramolecular transfer of a hydrogen atom from the carboxylic group to the NH2 group and a transfer chain of H atoms from the ammonium group to the hydroxy and water adsorbates. On the other hand, the experimental results predict that in the presence of water molecules both forms of glycine, neutral and zwitterion, are in equilibrium. On both surfaces of forsterite, the ammonia molecules enclosed in amorphous ice increase the adsorption energy of glycine on mineral surfaces with respect to glycine mixed with only water ice. Hence, the presence of ammonia enhances the stability of glycine on grains of dust. We find that the nondipolar surface has an inductive effect on the terminal COO− group of glycine to be coordinated with the Mg atom in a bridging monodentate−binuclear mode. The other peculiarity of this surface is that it can dissociate the water molecules. On the other hand, the adsorbed surface energy (γads) is a good parameter to evaluate the associative or dissociative character of the adsorption processes. Hence, in our model of simultaneous adsorption the dissociative process stabilizes the surface more than the associative one. In the second layered model where glycine is deposited onto surfaces covered with a thin amorphous ammonia−water ice layer, we observe a weak interaction of glycine with the frozen mineral surface (nondipolar). The glycine is only physisorbed onto mineral surfaces covered with dirty ice through hydrogen bonds of polar groups of the oxygen atoms of glycine and water. This result is in agreement with that reported in the theoretical and experimental work. The frequency calculated for H2O and NH3 molecules agrees with previous theoretical works. The amino acid has a strong

4. CONCLUSIONS The adsorption process of glycine can be affected by several components of cometary ice. In this study we have detailed, from a theoretical point of view, the effect of amorphous 26088



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(8) Cheung, A. C.; Rank, D. M.; Townes, C. H.; Thornton, D. D.; Welch, W. J. Detection of NH3 Molecules in the Interstellar Medium by Their Microwave Emission. Phys. Rev. Lett. 1968, 21, 1701−1705. (9) Charnley, S. B.; Rodgers, S. D. The End of Interstellar Chemistry as the Origin of Nitrogen in Comets and Meteorites. Astrophys. J. Lett. 2002, 569, L133−L137. (10) Bockelee-Morvan, D.; Crovisier, J.; Mumma, M. J.; Weaver, H. A. The Composition of Cometary Volatiles. In Comets II; Festou, M., Keller, H. U., and Weaver, H. A., Eds.; The University of Arizona: Tucson, AZ, 2004. (11) Zheng, W.; Jewitt, D.; Kaiser, R. I. Infrared Spectra of AmmoniaWater Ices. Astrophys. J., Suppl. Ser. 2009, 181, 53−61. (12) Cartwright, J. H. E.; Escribano, B.; Sainz-Diaz, C. I. The Mesoscale Morphologies of Ice Films: Porous and Biomorphic Forms of Ice under Astrophysical Conditions. Astrophys. J. 2008, 687, 1406. (13) Woon, D. E. Ab Initio Quantum Chemical Studies of Reactions in Astrophysical Ices: 2. Reactions in H2CO/HCN/HNC/H2O Ices. Icarus 2001, 149, 277−284. (14) Woon, D. E. Ab Initio Quantum Chemical Studies of Reactions in Astrophysical Ices 3. Reactions of HOCH2NH2 Formed in H2CO/ NH3/H2O Ices. J. Phys. Chem. A 2001, 105, 9478−9481. (15) Barrientos, C.; Redondo, P.; Largo, L.; Rayón, V. M.; Largo, A. Gas-Phase Synthesis of Precursors of Interstellar Glycine: A Computational Study of the Reactions of Acetic Acid with Hydroxylamine and Its Ionized and Protonated Derivatives. Astrophys. J. 2012, 748, 99. (16) Lattelais, M.; Pauzat, F.; Pilmé, J.; Ellinger, Y.; Ceccarelli, C. About the Detectability of Glycine in the Interstellar Medium. Astron. Astrophys. 2011, 532. (17) Belen, M.; Rodriguez-Lazcano, Y.; Galvez, O.; Tanarro, I.; Escribano, R. An Infrared Study of Solid Glycine in Environments of Astrophysical Relevance. Phys. Chem. Chem. Phys. 2011, 13, 12268− 12276. (18) Zanchet, A.; Rodríguez-Lazcano, Y.; Gálvez, Ó .; Herrero, V. J.; Escribano, R.; Maté, B. Optical Constants of NH3 and NH3:N2 Amorphous Ices in the Near-infrared and Mid-infrared Regions. Astrophys. J. 2013, 777, 26. (19) Moore, M. H.; Ferrante, R. F.; Hudson, R. L.; Stone, J. N. Ammonia−Water Ice Laboratory Studies Relevant to Outer Solar System Surfaces. Icarus 2007, 190, 260−273. (20) Rodriguez, J. A.; Kuhn, W. K.; Truong, C. M.; Goodman, D. W. A FT-IRAS Study of Ammonia Adsorbed on Ru(0001). Surf. Sci. 1992, 271, 333−339. (21) Thiam, M. M.; Ebrahimi, M. The Adsorption of Neutral Glycine Molecules on Ice Nanolayers. e-J. Surf. Sci. Nanotechnol. 2009, 7, 693− 698. (22) Rosado, M. T.; Duarte, M. L. T. S.; Fausto, R. Vibrational Spectra of Acid and Alkaline Glycine Salts. Vib. Spectrosc. 1998, 16, 35−54. (23) Sexton, B. A.; Mitchell, G. E. Vibrational Spectra of Ammonia Chemisorbed on Platinum (111): I. Identification of Chemisorbed States. Surf. Sci. 1980, 99, 523−538. (24) Amores, J. G.; Escribano, V. S.; Ramis, G.; Busca, G. An FT-IR Study of Ammonia Adsorption and Oxidation over Anatase-Supported Metal Oxides. Appl. Catal., B 1997, 13, 45−58. (25) Escamilla-Roa, E.; Moreno, F. Adsorption of Glycine by Cometary Dust: Astrobiological Implications. Planet. Space Sci. 2012, 70, 1−9. (26) Escamilla-Roa, E.; Moreno, F. Adsorption of Glycine on Cometary Dust Grains: IIEffect of Amorphous Water Ice. Planet. Space Sci. 2013, 75, 1−10. (27) Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1996, 77, 3865−3868. (28) Accelrys Inc.; Materials Studio, San Diego, CA, 2009. (29) Barnard, A. S.; Zapol, P. Effects of Particle Morphology and Surface Hydrogenation on the Phase Stability of TiO2. Phys. Rev. B 2004, 70, 235403.

frequency shift in the groups that interact with the mineral surface, i.e., NH2 and COOH terminal groups. In the nondipolar surface, the υ(CO) frequency indicates the adsorption kind of bridging monodentate−binuclear with a strong interaction with surface Mg cations. The COOH group of the adsorbed glycine shows bathochromic shifts with respect to free glycine molecule, as expected. Large frequency shifts are observed in CO stretching bands on both surfaces, probably due to the fact that the carboxylic group binds to the surface. Our calculations propose that the coordination in bridging the monodentate−binuclear mode is the most favored. Our calculated vibrational frequencies are similar to experimental and previous theoretical work for glycine adsorbed onto other surfaces. Taking into account that the adsorption process is produced in the solid−gas interphase (grain dust-adsorbates), our results suggest that the glycine molecule has a strong interaction with the mineral surface and this interaction increases with the cometary ice components. Hence, the amino acid can be in the deepest part of the cometary dust, and then probably the glycine molecule cannot be detected clearly in spectroscopic observations. We consider that these atomistic calculations can help us to understand from an atomic point of view the results obtained on glycine in the Stardust samples from comet 81P/ Wild2. These results can be useful to interpret future studies related to comet 67P/Churyumov−Gerasimenko, within the Rosetta mission.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work was supported by contracts AYA2009-08190, AYA2011-30613-C02-01, FQM-4555 (Proyecto de Excelencia, ́ and RNM-363. Authors thank Prof. F. Junta de Andalucia), Moreno for fruitful discussions. E. Escamilla-Roa is thankful to D. R. Esteso for their help in graphics.

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REFERENCES

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Effect of Amorphous AmmoniaâWater Ice onto Adsorption of Glycine

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