Diffusion-Reaction of Water Molecules in Angstrom Pores as Basic

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Diffusion-Reaction of Water Molecules in Angstrom Pores as Basic Mechanism of Biogenic Quartz Formation K. Sato,†,* K. Fujimoto,† M. Nakata,‡ and T. Hatta§ †

Department of Environmental Sciences, Tokyo Gakugei University, 4-1-1 Koganei, Tokyo 184-8501, Japan, Department of Astronomy and Earth Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501, Japan, § Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan ‡

ABSTRACT: The formation of biogenic silica quartz in the steady-state environment is a widespread phenomenon that is prerequisite for understanding biomineralization, diagenetic evolution, biogeochemical cycling, and reservoir formation, yet the mechanism is not fully understood. Here, the formation mechanism of silica quartz originated from diatom algae is investigated under low temperature/pressure conditions focusing on angstrom-scale pores. There exist 2 Å pores in amorphous silica acting as pathways of water diffusion with an activation energy of 2.3 eV. Water molecules react with highly reactive pore surfaces involving an energy cost of 1.9 eV, which triggers off the quartz formation. We show that the mechanistic theory of nucleation taking account of diffusion and reactions of water molecules in the angstrom-scale pores explains the long-term formation of biogenic silica quartz.

’ INTRODUCTION Biogenic silica has attracted much attention due to its pivotal importance for advancing earth sciences as well as the strong impact on ecological systems. As is well-known, silica is one of the most common minerals in earth’s crust, thus preserving an environmental history on its formation processes. Amorphous silica transforms to crystalline quartz through biochemical and geophysical processes on geological time scales in the steadystate environment as, e.g., low temperature and low pressure. This widespread phenomenon has stimulated a long history of diagenetic investigation for sequential stratigraphy and marine sediments.1
7 In addition, biogenic silica plays a crucial role in the global cycling of carbon, influencing on atmospheric carbon dioxide concentrations.8,9 A wealth of phytoplankton productivity of biogenic silica increases bacterial metabolism and diversity offering potential reservoirs in deep subsurface environment as ecosystems.10 Previous experiments focusing on water solution as, e.g., dissolution rate measurement, have indicated that the silica
water interaction causes long-term dissolution and subsequent precipitation implying the following characteristic signatures.11
15 1. The silica-water interaction takes place at a certain silica surface. 2. The transformation undergoes with thermally activated reaction. 3. Diffusion and reactions of water molecules limit the transformation at low temperatures. These elementary processes of light molecular system as water molecules have not been satisfactorily identified by diffraction and scattering techniques for amorphous silica without any specific surface structures. Thus, the formation mechanism of biogenic silica quartz under the steady-state conditions still remains puzzle. On the basis of the data of tracer diffusion experiments with tritiated water, it has been shown that water molecules diffuse r 2011 American Chemical Society

with a considerably low activation energy of ∼0.7 eV for amorphous silica.16 On the contrary, recent first principle calculation predicts more complex diffusion mechanism that an activation energy of water diffusion ranges from 0.8 to 2.2 eV depending on the sizes of angstrom-scale pores in amorphous silica.17,18 The calculations further predict that local chemical environments of pore surfaces cause different possible reactions with water molecules ranging activation energies from 0.3 to 5.9 eV. Dove et al. observed that the kinetics of amorphous silica dissolution exhibits a strong exponential dependence on chemical-driving force, in which specific surface structures on atomic scale have to be considered.12 Here, we focus on the structural variations of angstrom-scale pores present in biogenic silica originated from diatom algae aside from water solution to gain an insight into the mechanism of long-term and low-temperature/pressure quartz formation. The purpose of the present work is to answer the following questions: 1. Does biogenic amorphous silica possess angstrom-scale pores? 2. Is the angstrom-scale pore in biogenic silica different from that of conventional inorganic silica? 3. Do the angstrom-scale pores act as the pathways of water diffusion? 4. Do surfaces of the angstrompores in the biogenic amorphous silica react with water molecules? 5. Does the formation of crystalline quartz from biogenic amorphous silica follow the classical nuclear theory?

’ EXPERIMENTAL SECTION The cell wall of diatom algae is known to contain silica. We thus employed amorphous silica originated from algae frustules Received: June 6, 2011 Revised: July 29, 2011 Published: August 09, 2011 18131

dx.doi.org/10.1021/jp205299q | J. Phys. Chem. C 2011, 115, 18131–18135

The Journal of Physical Chemistry C collected from Mariana Trench, as starting materials. Hydrothermal reaction on a 70-day time scale was performed in the temperature range from 383 to 443 K in a cylindrical Teflon vessel. Silica products, chemical compositions of water solution, and oxygen bonding energies were examined by X-ray diffraction (XRD), inductively coupled plasma (ICP) technique, and X-ray photoelectron spectroscopy (XPS), respectively. The sizes of angstrom-pores and their intensities were investigated by positron annihilation lifetime spectroscopy. A fraction of energetic positrons injected into samples forms the bound state with an electron, positronium (Ps). Singlet para-Ps (p-Ps) with the spins of the positron and electron antiparallel and triplet ortho-Ps (o-Ps) with parallel spins are formed at a ratio of 1: 3. Hence, three states of positrons: p-Ps, o-Ps, and free positrons exist in samples. The annihilation of p-Ps results in the emission of two γ-ray photons of 511 keV with lifetime ∼125 ps. Free positrons are trapped by negatively charged parts such as polar elements and annihilated into two photons with lifetime ∼450 ps. The positron in o-Ps undergoes two-photon annihilation with one of the bound electrons with a lifetime of a few ns after localization in angstrom-scale pores. The last process is known as o-Ps pick off annihilation and provides information on the free volume size R through its lifetime τ3 based on the Tao-Eldrup model:19,20    R 1 2πR
1 sin τ3 ¼ 0:5 1
þ ð1Þ R0 2π R0 where R0 = R + ΔR, and ΔR = 0.166 nm is the thickness of homogeneous electron layer in which the positron in o-Ps annihilates. The positron source (22Na), sealed in a thin foil of Kapton, was mounted in a sample-source-sample sandwich. Positron lifetime spectra were numerically analyzed using the POSITRONFIT code.21 Pore surfaces were investigated by means of momentum distributions of o-Ps pick-off annihilation localized at angstrom-scale pores. This momentum spectroscopy is based on the principle that if the positron-electron annihilation accompanies a longitudinal momentum p, the resulting annihilation γ rays are Doppler shifted from m0c2 by ( cp/2. Here, mo and c are the electron rest mass and velocity of light, respectively. Measurements of the Doppler shifts by γ-ray energy spectroscopy with high purity Ge detector make it possible to obtain information on the momentum distribution of the positron-electron annihilation pairs. The momentum distribution of o-Ps is broadened centered at 511 keV because the pick-off annihilation is influenced by electrons bound to the surrounding molecules.22,23 Thus, the momentum distribution of o-Ps pick-off annihilation provides the information on electronic states of angstrom-scale pore surfaces. The momentum distribution of o-Ps pick-off annihilation was extracted by time-resolved momentum measurements of positron-electron annihilation photons using recently developed positron-age-momentum correlation (AMOC) spectroscopy.24 Taking the ratio of the central area over (
3.6 to +3.6)  10
3 m0c to the total area of the momentum spectrum, o-Ps pick-off annihilation was parametrized.25 We call it poresurface parameter that was recently found to be sensitive to light elements on pore surfaces as, e.g., oxygen.24

’ RESULTS AND DISCUSSION Figure 1 shows XRD patterns observed for materials reacted at 423 K for 336 h, 672 h, 1176 h, and 1680 h. Structural evolution

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Figure 1. X-ray diffraction patterns observed for materials hydrothermally reacted at 423 K for 336 h, 672 h, 1176 h, and 1680 h. XRD peaks indexed to the cristobalite and quartz are marked with C and Q, respectively.

Figure 2. Oxygen 1s XPS spectra observed for materials hydrothermally reacted at 423 K for 0 h, 336 h, 672 h, 1176 h, and 1680 h. Arrows are drawn for guiding the eye.

toward crystalline quartz with increasing the reacted time can be seen in the variation. The diffraction pattern at 336 h is of a typical amorphous structure, which maintains up to 672 h. XRD peaks arising from the quartz phase begin to appear together with those from the cristobalite phase at 1176 h. The peaks of cristobalite phase disappear at 1680 h and the quartz phase is dominantly formed. Figure 2 shows oxygen 1s XPS spectra observed for materials reacted at 423 K for 0 h, 336 h, 672 h, 1176 h, and 1680 h. All of the oxygen 1s peaks are largely shifted toward the lower binding energy than of conventional inorganic SiO2 glass (∼ 531.9 eV), signifying the presence of nonbridging oxygen bonds more than SiO2 glass. At 336 h, full width at half-maximum (fwhm) of the spectrum increases by ∼15%, whereas no chemical shift is observed. This demonstrates the formation of a variety of oxygen chemical bonds as, e.g., silanol. Although no significant change is observed in XRD patterns, oxygen 1s peak is slightly shifted toward higher binding energy fwhm being constant at 672 h. The chemical shift becomes more prominent with the reduction of fwhm by ∼10% 18132

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The Journal of Physical Chemistry C

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Figure 4. (a) Reaction-time variations of pore-surface parameter at 383 K (gray circles), 403 K (red triangles), 423 K (green squares), and 443 K (blue diamonds). Solid lines denote the results of the fits by an exponential with a decay constant kr. (b) Logarithms of decay constants as a function of inverse temperature (purple inverse triangles). Figure 3. (a) Reaction-time variations of pore intensities I3 at 383 K (gray circles), 403 K (red triangles), 423 K (green squares), and 443 K (blue diamonds). Solid lines denote the results of the fits by an exponential with a decay constant kf. (b) Logarithms of decay constants as a function of inverse temperature obtained by the present pore analyses (purple inverse triangles) and by the ICP technique (stars), respectively.

at 1176 h, where XRD peaks of quartz and cristobalite appear. It is known that the angle of Si
O
Si in cristobalite is larger than in amorphous silica at low temperatures. The larger angle causes the lower electron density around oxygen atoms, leading to the chemical shift toward the higher binding energy. The chemical shifts observed with increasing reaction time to 1176 h are thus attributable to the formation of cristobalite. The decrease of fwhm is due to dissociation of instantaneous bonds to form cristobalite and quartz. At 1680 h, oxygen 1s peak is shifted back to the lower binding energy with a slight reduction of fwhm due to the disappearance of cristobalite with larger Si
O
Si angle, in agreement with XRD. Positron lifetime spectroscopy for amorphous silica yields three components, of which the longest-lived component τ3 of ∼1.6 ns is attributable to pick-off annihilation of o-Ps localized in angstrom-scale pores of amorphous matrix. The pore size is evaluated to be ∼2 Å through the lifetime component τ3 based on the Tao-Eldrup model.19,20 Such a microscopic pore could not be observed for aperiodic amorphous silica consisting of light elements by conventional porosimetric techniques as, e.g., mercury intrusion porosimetry, gas absorption porosimetry, and even high-resolution TEM. No systematic changes are observed in the lifetime τ3 when the quartz formation proceeds at longer reaction time. In light of the fact that no long lifetime component τ3 is observed in silica polymorphs with high crystallinity as, e.g., crystalline quartz,26 angstrom-scale pores are located not in the quartz phase but in the intergranular amorphous regions. Figure 3 (a) shows reaction-time variations of pore intensities I3 at 383 K, 403 K, 423 K, and 443 K. The pore intensities decrease with increasing the reaction time up to 1680 h (70 days) at the lower temperature of 383 K. The decreasing tendency with the reaction time becomes increasingly prominent when the

temperature is raised up to 443 K. The formation of quartz in the amorphous matrix creates the intergranular amorphous regions and its growth reduces the volume fraction of intergranular amorphous regions. It is thus reasonable that angstrom-scale pores in the intergranular amorphous regions decrease together with the quartz formation. Of great importance here is that the quartz formation can be now visible with respect to the structural modification of silica itself apart from water solution. Good fits of isotherms are obtained by an exponential with a decay constant kf, as indicated with solid lines. In Figure 3(b), the logarithms of decay constants are plotted as a function of inverse temperature. It follows the Arrhenius law demonstrating that the quartz formation is governed by the thermally activated reaction. From temperature variation, the activation energy of quartz formation is derived to be 4.2 eV. For comparison, the Arrhenius plot obtained from the Si composition of water solution determined by the ICP technique is shown in Figure 3(b) (see stars). Obviously, the Arrhenius plot lacks precision in assessing the activation energy of quartz formation. The pore-surface parameters at 383 K, 403 K, 423 K, and 443 K are shown in Figure 4(a) as a function of reaction time. As is detailed in our former manuscript,24 the decrease of o-Ps parameters with increasing reaction time are a consequence resultant from increased oxygen atoms incorporated with pore surfaces. Thermally activated reactions of water molecules at pore surfaces can be well seen similarly to that of quartz formation (see Figure 3 (a)). The logarithms of decay constants obtained from an exponential fit are plotted as a function of inverse temperature in Figure 4 (b). From the temperature variation the activation energy of reaction between water molecules and pore surface is derived to be 1.9 eV, which is lower than that of quartz formation. On the basis of a classical nuclear theory, temperaturedependent quartz formation rate J is modeled as follows:   Ef ð2Þ JðTÞ ¼ Aexp
kT where A, T, Ef, and k are pre-exponential factor, temperature, activation energy of quartz formation, and Boltzmann constant, respectively. Rewriting Ef in terms of diffusion of water molecules 18133

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The Journal of Physical Chemistry C through angstrom pores and reaction of water molecules at pore surfaces gives the following:     Ed Er JðTÞ ¼ Aexp
exp
ð3Þ kT kT where Ed and Er are activation energies of water diffusion through angstrom-scale pores and water reaction at pore surfaces, respectively. Applying eqs 2 and 3 to the Arrhenius plots in Figures 3 (b) and 4 (b), Er, Ed, and Ef are determined to be 1.9 eV, 2.3 eV, and 4.2 eV, respectively. Here, we compare above activation energies with theoretical prediction for lack of experimental data. According to first principle calculations,17,18 the activation energy of water reaction at pore surfaces is variable ranging 0.3
5.9 eV with possible chemical environment of pore surfaces. The obtained activation energy Er is relatively low while it is within the calculated range. As was already mentioned, XPS suggests that there exist nonbridging oxygen bonds for the present samples more than typical inorganic SiO2 glass. It is thus anticipated that oxygen atoms incorporated with pore surfaces of biogenic silica are highly reactive with dangling bonds and water molecules can easily form other bonds as, e.g., silanol. This is further supported by the increase of fwhm of XPS spectrum by ∼15% at the reaction time of 336 h without any chemical shift. The activation energy of water reaction at pore surfaces evaluated here is therefore concluded to be reasonable. The calculated activation energy of water diffusion through interconnected pores begins to increase rapidly at the pore radius of 3 Å and reaches as high as 2.2 eV at the radius of 2 Å. The activation energy of water diffusion Ed evaluated from Er and Ef is in excellent agreement with the above calculation. This validates an application of the nuclear theory taking account of diffusion-reaction of water molecules to the long-term quartz formation observed in the present study. Combining the results of XRD and XPS with angstrom-scale pore analyses, the following mechanism of biogenic quartz formation can be drawn. There exist highly reactive pores with the size of 2 Å in the present biogenic amorphous silica. Water molecules diffuse through the angstrom-scale pores in the amorphous matrix with the activation energy of 2.3 eV. Pores surfaces are immediately hydroxylated by water molecules, in which silanol groups are dominant. The silanol groups are ionized producing mobile protons that associate/dissociate with the pore surfaces. Resultantly, the electrical double layer is formed inducing reorientation of water molecules due to ionic conductivities. The formation of electrical double layer inside the angstrom-scale pores in amorphous silica is also evidenced by the data of sum frequency generation infrared (SFG-IR) spectroscopy27 together with recent nanofluidic studies.28 The directional water molecules affect reactions at pore surfaces, triggering off the nucleation of crystalline quartz with the activation energy of 1.9 eV. Water molecules initially form a variety of instantaneous bonds relevant to oxygen at pore surfaces. The oxygen chemical bonds partially transform to that of cristobalite with larger Si
O
Si angle and then to that of quartz. The cristobalite phase disappears presumably to be closely packed structure for stabilization and, finally, the quartz phase becomes dominant involving the total energy cost of 4.2 eV.

’ CONCLUSIONS We succeeded in studying the static formation mechanism of biogenic silica quartz under low temperature/pressure conditions focusing on the angstrom-scale pores. The fraction of

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angstrom-scale pores and their surface structures are specifically probed by positronium annihilation spectroscopy. Water molecules diffuse through 2 Å pores in amorphous silica with an activation energy of 2.3 eV. They react with highly reactive pore surfaces involving an energy cost of 1.9 eV, which triggers off the quartz formation. The long-term formation of biogenic silica quartz follows the mechanistic theory of nucleation taking account of diffusion and reactions of water molecules in the angstromscale pores.

’ AUTHOR INFORMATION Corresponding Author

*E-mail: [email protected].

’ ACKNOWLEDGMENT The authors are indebted to Dr. Ikehara (AIST) for supplying starting materials. Discussion with Prof. Shikazono (Keio University) is gratefully appreciated. This work was partially supported by a Grant-in-Aid of the Japanese Ministry of Education, Science, Sports and Culture (Grant Nos. 21540317 and 23740234). ’ REFERENCES (1) Zhou, X.; Xia, S.; Lu, Z.; Tian, Y.; Yan, Y.; Zhu, J. J. Am. Chem. Soc. 2010, 132, 6932. (2) Kellermeier, M.; Melero-Garcia, E.; Glaab, F.; Klein, R.; Drechsler, M.; Rachel, R.; García-Ruiz, J. M.; Kunz, W. J. Am. Chem. Soc. 2010, 132, 17859. (3) Vorhies, J. S.; Gaines, R. Nat. Geosci. 2009, 2, 221. (4) Lepot, K.; Benzerara, K.; Brown, G. E., Jr.; Philippot, P. Nat. Geosci. 2008, 1, 118. (5) Diaz, J.; Ingall, E.; Nelson, C. B.; Paterson, D.; de Jonge, M. D.; McNulty, I.; Brandes, J. A. Science 2008, 320, 652. (6) Allwood, A. C.; Grotzinger, J. P.; Knoll, A. H.; Burch, I. W.; Anderson, M. S.; Coleman, M. L.; Kanik, I. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 9548. (7) Bansal, V.; Ahmad, A.; Sastry, M. J. Am. Chem. Soc. 2006, 128, 14059. (8) Kohfeld, K. E.; Qu
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