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. 2025 Sep 14;10(37):42218–42223. doi: 10.1021/acsomega.5c00728

Simulation Study on Adsorption Characteristics of Aspartate on the Calcite (104) Surface

Pengpeng Shang 1, kunpeng Dou 1, Chun Li 1, Dabo Guo 1, Guang Yuan 1,*
PMCID: PMC12461421  PMID: 41018608

Abstract

The adsorption properties of H2O and aspartate (ASP) molecules on the calcite (104) surface were calculated by the density functional theory (DFT) method, and the adsorption configurations of different surface structures were compared. The results show that the adsorption of ASP molecules on the surface of calcite is stronger than that of H2O molecules, and it is easier to bind to the surface of calcite. The adsorption energy of the ASP molecule on the surface of the steps is obviously higher than that on the terraces, which is more conducive to the adsorption of amino acids. These results contribute to understanding the mechanism by which ASP molecules participate in the formation of calcite structures in organisms.

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1. Introduction

Biomineralization is a complex process, and factors such as organic matter, inherent properties of crystals, and environment have important influences on the biomineralization process. − Calcite is one of the products of biomineralization and is an important part of the bones, teeth, and shells of marine organisms. Under biological control, the surface of the calcite skeleton produced by echinoderms is curved like a sponge needle, but the formation and stabilization mechanism of this structure remains unclear. A two-scale TPMS (three-period minimum surface) structure was discovered in the calcite skeleton of Protoreaster nodosus, and proposed that symmetry in the formation of such calcite skeletons is regulated by interactions with biomolecules. The step structure of calcite with a height of 0.3 nm on the molecular scale in the experiment is consistent with the height of the single-layer molecular calcite (104) surface. The formation of biomaterials is regulated by biomolecules, in which amino acids play an important role. Aspartate (ASP) can participate in the formation of biogenic minerals. At the nucleation site of calcifying organisms, ASP-rich macromolecules can widely participate in regulation and affect the formation of biological minerals. It is found in the experiment that ASP can affect the direction and width of calcite steps, and has a direct impact on the growth form of calcite. , The oxygen atom of carboxylic acid in ASP can be directly bound to the acute step on the surface of calcite, and this specific binding changes the free energy at the edge of the step, resulting in the change of macroscopic crystal shape.

Molecular simulations are increasingly used to study the crystal forms of calcite in contact with water and the growth or inhibition of minerals. The dynamic evolution process of calcite and biomolecular systems was provided through molecular dynamics (MD) calculation, so as to study the equilibrium conditions and mechanical properties of the composite system. The density functional theory (DFT) method can provide a finer structure, which is a verification and supplement to the experiment and MD calculation. , Three different common calcite surfaces were constructed, namely terrace, acute step, and obtuse step, and the adsorption behavior of small surfactant molecules on the edge of calcite steps was explored by using DFT methods, and compared their adsorption properties. − Therefore, it is very important to compare the adsorption patterns and interaction strengths of small organic molecules and water on the surface of calcite.

In this work, adsorption models of single ASP molecules on calcite terraces, acute steps, and obtuse steps were constructed and compared with the adsorption of H2O molecules. As an important small molecular component in organisms, ASP molecules bind to the specific surface of calcite, which can regulate the surface growth of calcite and further affect the macroscopic shape of calcite in organisms. These results help to understand the formation process of biological minerals and provide new ideas for the manufacture of organic–inorganic hybrid materials.

2. Methodology and Model

2.1. Surface Model

Figure shows the structure model of the calcite surface, the H2O molecule, and the ASP molecule. Calcite step surfaces have three types: terrace, acute, and obtuse steps. The structural parameters of the calcite protocell are a = b = 5.05 Å, c = 17.30 Å, α = β = 90°, and γ = 120°, which are basically consistent with the experimental lattice parameters. The surface is constructed by the calcite primary cell (104), and the two sides are composed of alternating cation and cation along the directions of [4 8 1̅] and [4̅ 4 1]. The slab consists of four layers of atoms; the bottom layer is fixed, and steps are constructed by removing some of the atoms. As shown in Figure (a), the angles of calcite step edges are 78° and 102° respectively, which are consistent with the experimental results. , The O–H bond length of the H2O molecule is 1.11 Å, and the bond angle is 109.47°. The amino bond length of the ASP molecule is 1.46 Å, and the bond angle is 110.37°. The bond length of the carboxyl group in the main chain is 1.53 Å, and the bond angle is 109.36°. The branched carboxyl group is 1.51Å, the bond angle is 113.77°, and the bond lengths of the CO bonds are all 1.22 Å. In order to avoid the interaction along the aperiodic direction, a 20Å vacuum layer is arranged in the vertical direction.

1.

1

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Molecular structure model: (a) Side view of the calcite slabs; (b) H2O molecular model; (c) ASP molecular model. The green ball represents the Ca atom, the red ball represents the O atom, the gray ball represents the C atom, and the blue ball represents the N atom.

2.2. Computational Methodology

The structural optimization was determined using the Quantum ATK (S-2021.06) software package in the framework of the DFT method. , The cutoff energy is set to 3.4 × 103 eV. Perdew–Burke–Ernzerhof generalized gradient approximation (PBE-GGA) was used to describe the commutation-correlation interaction. All atoms are described using the Dojo pseudopotential with a medium base set. The 2 × 1 Monkhorst–Pack scheme was adopted in the Brillouin region. The van der Waals interaction is explained using the DFT-D3 method. The convergence criterion for structural optimization is set to 0.03 eV/ Å.

3. Results and Discussion

3.1. Optimized Structure and Adsorption Energy

The optimized minimum energy configuration, adsorption energy, and bonding information on H2O and ASP molecules to the calcite surface are shown in Table . The construction of the ASP molecular adsorption model takes into account that the amino group and one of the carboxyl groups can interact with the calcite surface at the same time, and a total of 10 different initial models are constructed on three different surfaces (2 terraces, 4 acute steps, 4 obtuse steps). The adsorption energy is calculated by the following formula:

Eads=E(slab+molecule)−Eslab−Emolecule 1

where E slab is the total energy of the slab, E molecule is the total energy of the isolated aspartate molecule, and E (slab+molecule) is the total energy of the slab with adsorbed aspartate molecule. In all adsorption systems, the adsorption energy was negative and could be spontaneous. The absolute value of the adsorption energy of H2O molecules on the acute steps of calcite is greater, and the adsorption is stronger than that on terraces and obtuse steps, which is consistent with previous studies.

1. Optimized Minimum Energy Configuration, Adsorption Energy, and Bonding Information of H2O Molecules and ASP Molecules to the Calcite Surface.

3.1.

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The adsorption energy of ASP molecules on the three different calcite surfaces of terrace, acute step, and obtuse step was higher than that of H2O molecules. In the terraces, the adsorption energy of H2O molecules was −1.38 eV (T-H2O), and the maximum adsorption energy of ASP molecules was −2.23 eV (T-ASP1), indicating that the surface of calcite is more inclined to combine with ASP molecules. When ASP molecules and H2O molecules were adsorbed on the surfaces of three different calcite slabs, the adsorption on the step surface was better than that on the terrace, and the absolute value of the adsorption energy on the acute step was larger. Among them, the adsorption energy of H2O molecules was −2.44 eV (A-H2O), and the maximum adsorption energy of ASP molecules was −4.51 eV (A-ASP3). The edge of the acute step was more likely to combine with the two small molecules. Second, on the obtuse step surface, the adsorption energy of H2O molecules was −1.51 eV (O-H2O), and the maximum adsorption energy of ASP molecules was −3.03 eV, which also shows favorable adsorption for small molecules.

In A-H2O, the atom of the H2O molecule simultaneously connected with the Ca atom on the upper layer of the step (Ca1) and the Ca atom on the lower layer of the step (Ca2), forming a more stable double-bridge structure. The amino group and one of the carboxyl groups of the ASP molecule are bonded to the exposed Ca atoms on the calcite surface, similar to previous studies. , The atomic distance between the Ca atom on the calcite surface and the carboxyl O atom or amino N atom in the ASP molecule was 2.3∼2.7 Å, which accords with the usual bond length of the Ca–O bond and the Ca–N bond. The acute step is a particularly favorable adsorption site. In ASP-A3, when the carboxyl group of the ASP molecule approached the step, the O atom could approach two calcium atoms simultaneously. While forming a Ca–O bond (2.56 Å) with the Ca atom on the upper layer of the step (Ca1), it also formed a Ca–O bond (2.49 Å) with the Ca atom at the lower edge of the step (Ca3). In this case, the absolute value of adsorption energy is the largest, and the adsorption configuration is more stable.

In order to visualize the deformation of the calcite step surface and the ASP molecule before and after adsorption, the bond angle and bond length of the calcite surfaces and the ASP molecules were determined. When the ASP molecule was not adsorbed, the angle between the upper and lower layers of the calcite acute edge is 78.15° and the obtuse edge is 101.85°, respectively, and the angle of the step edge changes in different degrees after the combination with the ASP molecule. At the edge of the acute step (A-ASP3), when the carboxyl group combines with Ca at the lower layer of the step and the amino group combines with Ca at the upper layer of the step, the change in the edge angle is more obvious, increasing by 8.59° and 9.54°, respectively. In contrast, when the carboxyl group combines with the two Ca atoms on the upper and lower layers of the step, its influence on the acute Angle step is very small, with only increases of 0.39° and 0.30°. It seems that ASP molecules can naturally bind to the acute edge of calcite without affecting the calcite’s own arrangement. The angles of the obtuse edges all changed significantly, and the deformation caused by the combination of the main chain carboxyl group and the obtuse edges was relatively small.

After interacting with the surface of calcite, the bond lengths of the functional groups of ASP molecules connected to the whole change little, but the bond angles change by 0.05∼3.67°, indicating that the ASP molecules themselves can adapt to the combination with the surface of calcite through shape changes. In addition, the length change of the CO bond was measured because of the direct interaction between the O atom in the carboxyl group and the calcite edge Ca atom. In most cases, the CO bond did not change significantly, but after the interaction of ASP molecules with the A-ASP3, the CO bond was significantly elongated, increasing by 0.05 Å, and O1 is closer to the calcite surface. According to the bonding information on the ASP molecule and the calcite surface, O1 could bind to two Ca atoms above and below the step at the same time in these two adsorption configurations, and this deformation seems to be a change to form a more stable binding mode. ASP molecules could better interact with calcite edges through rotation of the bond angles and stretching of the bond lengths to form stable structures.

3.2. Electron Transfer and Density of the Energy States

The electron density difference of the adsorption configurations of the ASP molecule on the surface of calcite is shown in Figure . The electron density difference is obtained by subtracting the electron density of the ASP molecule and the calcite plate from the charge density of the adsorption system, and is plotted at an equivalent face value of 0.005 e/Å3.

Δρ=ρ(slab+molecule)−ρslab−ρmolecule 2

where ρslab is the electron density difference of the slab, ρmolecule is the electron density difference of the isolated aspartate molecule, and ρ(slab+molecule) is the electron density difference of the slab with adsorbed aspartate molecule.

2.

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Electron density difference diagram of the adsorption configuration of the ASP molecule on the surface of calcite (taking T-ASP1, A-ASP3, and O-ASP1 as examples), equivalent to Δρ = +0.005e (red) and −0.005e (blue) electron density difference iso surface.

After the interaction between the ASP molecule and the calcite surface, the electron transfer was obvious. Similar to previous adsorption of ASP on other surfaces, the interaction is caused by amino and carboxyl groups, and electrons are transferred from the surface to the ASP molecule. , In the adsorption configuration, the red iso surfaces (electron-rich region) mainly exist between Ca–O and Ca–N bonds and around the O and N atoms of the ASP molecule. The blue iso surfaces, or electron loss regions, are mainly located outside the Ca atom on the calcite surface, that is, near the Ca atom interacting with the ASP molecule. As shown in Figure , among Ca–O atoms, due to electronegativity, electrons tended to gather around the O atom near the ASP molecule, the electron density near the O atom increased, and the electron density near the Ca atom decreased. At the same time, electron density accumulated along the Ca–O bond axis, electron sharing existed in the bond region, and covalent components existed, but ionic properties were still dominant. Among the Ca–N bonds, electrons were mainly clustered around the N atom and in the direction of the Ca–N bond axis, which was covalently shared. Electrons were missing around Ca atoms, and positive charges accumulated. The main coordination is covalent but also has some ionic properties.

Steps increased the contact and interaction between the ASP molecule and the calcite surface. In the configuration of acute edge interaction between the ASP molecule and calcite (A-ASP3), the iso surfaces were obviously larger than the others, and the electron transfer was greater. According to the information given by the binding bond length, when the ASP molecule was adsorbed to the A3 and A4 steps, the O atom interacted with the two Ca atoms above and below the steps, and this bonding mode, dominated by an ionic bond, can be stabilized by electrostatic action in polar environments (such as aqueous solution). In addition, in the adsorption configurations of A3-ASP, and O1-ASP, when the carboxyl terminal H atom of ASP molecule was close to the O atom on the surface of calcite, there was also a red iso surface between them, and the electrons are concentrated between the O–H atoms; the O atom showed electronegativity due to its higher electronegativity.

Taking A-ASP3 with the largest absolute value of adsorption energy as an example, Figure shows the density of states (DOS) of the atoms before and after adsorption. The adsorption bonding between the ASP molecule and calcite leads to the redistribution of electron structure, which leads to the obvious change of atomic orbital state density before and after adsorption. In the original DOS state, Ca atomic orbitals contributed some electron states in the lower energy range. When the carboxyl and amino groups of aspartate form Ca–O and Ca–N bonds with Ca atoms, the atomic orbitals of Ca are mixed with the atomic orbitals of O and N atoms of ASP. The p orbitals of O atoms contributed to the DOS after adsorption, and the Ca atoms appeared with small peaks in the energy range of bonding orbitals, indicating that the d orbitals of Ca atoms participate in bonding. In the unadsorbed free ASP molecule, the O atom of the carboxyl group contributed some p orbital electron states in the low energy region, and the N atom of the amino group contributed some s and p orbital electron states in the medium energy region. When ASP molecules were adsorbed onto the surface of calcite, the p orbitals of O atoms would mix with Ca atoms, resulting in the energy shift of carboxyl O atoms, and a new peak in the low energy region. The electron state of the N atom was shifted in the higher energy region in DOS, forming a new electron state. The O and N atoms of ASP changed their orbital state density, especially when their orbitals are mixed with the orbitals of Ca atoms; new peaks or shifts of existing peaks appeared in the DOS map. The DOS comparison before and after adsorption can obviously reveal the energy level redistribution of atomic orbitals and the change of electronic structure after the adsorption of aspartic acid on the surface of calcite.

3.

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DOS diagram of Ca1, Ca2, Ca3, O1, and N atoms in the adsorption configuration of A3-ASP3 before and after adsorption.

Figure shows the DOS of the three interacting atomic pairs in the A-ASP3 adsorption configuration. The Ca–O and Ca–N bonds formed by the carboxyl group and the amino group of the ASP molecule and the Ca atoms on the calcite surface significantly change the state density of the atomic orbitals. After adsorption of the ASP molecule, Ca atoms on the surface of calcite produced a new peak value in the low energy region; especially, the interaction with O and N atoms led to obvious changes in the electronic states of Ca. On the surface of calcite, the d orbitals of Ca atom and p orbitals of carboxyl O atom, which were bound to the O atom in ASP, overlapped in the vicinity of −4.73, −3.85 and 1.23 eV; the d orbitals of Ca atom and p orbitals of N atom, which were bound to the N atom in ASP, partially coincided around −4.32, −3.98, and 3.84 eV. The presence of hybrid peaks confirms that the d orbitals of Ca are involved in bonding with the p orbitals of N atom and O atom, respectively, and that both amino and carboxyl groups interact with the calcite surface calcium. When the ASP molecule interacted with calcite at an acute angle, the O1 of the ASP molecule could combine with Ca1 and Ca3 on the upper and lower surfaces at the same time. Comparing the DOS diagram of the two and the O1 atom, they had similar orbital coincidence, which confirms that the O1 atom can bridge with the upper and lower surfaces at the same time to form a stable structure.

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DOS diagram of three interacting atoms in the A-ASP3 adsorption configuration.

4. Conclusions

The fine structures of H2O and ASP molecules adsorbed on the calcite step surface were calculated and analyzed by the DFT method. The amino group and two carboxyl groups of the ASP molecule can combine with Ca atoms on the surface of calcite and form an adsorption configuration with multiple chemical bonds. Compared to H2O molecules, the surface of calcite was more inclined to bind to ASP molecules, resulting in a more stable structure. The step edge increases the contact between the ASP molecule and the calcite surface, which is more conducive to the formation of a stable configuration with multiple bonding. The bonding between ASP molecules and the surface calcite was conducive to the adsorption of aspartic acid molecules according to the change in electron density. Amino acids were adsorbed on the material to modify the surface, giving the biomaterial a specific shape. Our findings may have potential implications for designing effective material surface treatments for biomedical applications.

Acknowledgments

This work was supported by the National Key Research and Development Program of China (2024YFB3612304), Ministry of Education of the People's Republic of China (202364009), Key Technology Research and Development Program of Shandong Province (2023CXPT101).

The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.

The authors declare no competing financial interest.

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