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Definition of the Pnictogen Bond: A Perspective

Capture Mechanism of Cadmium in Agricultural Soil Via Iron-Modified Graphene

College of Agronomy, Hunan Agricultural University, Changsha 410128, China
Department of Physics, National University of Defense Technology, Changsha 410128, China
College of Resource and Environmental, Hunan Agricultural University, Changsha 410128, China
Hunan Provincial Key Laboratory of Efficient and Clean Utilization of Manganese Resources, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
School of Chemistry and Materials Science, Hunan Agricultural University, Changsha 410128, China
School of Energy and Environment, Southeast University, Nanjing 211189, China
Authors to whom correspondence should be addressed.
Inorganics 2022, 10(10), 150;
Received: 25 August 2022 / Revised: 19 September 2022 / Accepted: 20 September 2022 / Published: 22 September 2022
(This article belongs to the Section Inorganic Materials)


Cadmium (Cd) contamination in agricultural soils has caused extensive concern to researchers. Biochar with iron-compound modifications could give rise to the synergistic effect for Cd restriction. However, the related capture mechanism based on physicochemical properties is unclear. In this study, first principles calculations are proposed to explore the adsorption ability and potential mechanism of the ferric hydroxide modified graphene ([email protected]) for capturing CdCl2. The simulation results show that the adsorption energy to CdCl2 could enhance to −1.60 eV when Fe(OH)3 is introduced on graphene. Subsequently, analyses of electronic properties demonstrated a significant electron transfer between Cd s-orbital and O p-orbital, thereby leading to strong adsorption energy. This theoretical study not only identifies a powerful adsorption material for Cd reduction in agricultural soils and reveals the capture mechanism of [email protected] for Cd but also provides a foundation and strategy for Cd reduction in agricultural soils.
Keywords: iron-modified biochar; cadmium; first principles calculation; capture mechanism; density functional theory iron-modified biochar; cadmium; first principles calculation; capture mechanism; density functional theory

1. Introduction

With recent rapid developments and increased industrial emissions, cadmium (Cd) contamination is becoming a serious concern in east and south Asia, especially in China, India, and Thailand [1,2,3,4]. Here, until 2005, approximately 1.3 × 105 ha of agricultural soils in China were reported to be contaminated by Cd [5]. It is well known that Cd is a non-essential substance for plants; however, it is easily accumulated in agricultural crops [6,7,8,9]. For example, paddy rice can uptake Cd easily, and straw is the main accumulation region for Cd. A wide number of rice straws have been reportedly polluted by Cd every year in China [6,10]. In 2016, more than 10% of rice samples from rice markets exceeded the China National Standard for food contamination of Cd (<0.2 mg kg−1) [11]. Furthermore, due to the 30 year biological half-life of Cd, it has the potential to cause serious medical conditions such as cancer and Itai-Itai disease [12,13,14]. Thus, it is necessary to reduce the availability of Cd in agricultural crops and consequently to the human system.
To date, in situ metal stabilization has raised considerable concern due to its high effect on reducing the bioavailability and toxicity of heavy metals in short periods [15,16,17]. Among them, biochar from pyrolysis with limited oxygen has an irregular aromatic structure, multi-layered accumulation forms, and unique physicochemical properties, which make it a great candidate for soil amendments to inhibit Cd in soils [18,19,20,21]. For instance, Luo et al. demonstrated that corncob biochar could significantly increase the total nitrogen and organic matter content of the soil while stabilizing the availability of arsenic (As) and Cd in soil [22]. Furthermore, iron-based materials could reduce the efficiency of Cd by changing the physicochemical property of Cd [23,24]. Compared with pure biochar treatment, hybrid soil amendments of biochar and inorganic materials containing iron are better for reducing the Cd contamination of agricultural soils [18,25,26]. Qiao et al. reported that zero-valent iron (ZVI)-biochar could reduce Cd contamination in agricultural soils effectively [27]. Yin et al. reported that Fe-modified biochar reduced the accumulation of As and Cd in rice by reducing soil acidification [28]. However, the capture mechanism of Fe-modified biochar on Cd physicochemical systems has rarely been reported. Therefore, clarifying the capture mechanism of Fe-modified biochar on Cd is of paramount importance.
In this study, graphene (G) was used as the substrate to emulate the biochar. Graphene and its ferric hydroxide modification ([email protected]) were taken as the research objects to explore the capture mechanism with CdCl2 by first principles calculations. First, the structural and electronic property differences between G and [email protected] were checked. Then, the adsorption ability of G and [email protected] with CdCl2 were identified. Moreover, inherent changes in electronic properties and charge transferability were demonstrated. These findings show that there is a significant charge transfer between [email protected] and CdCl2, which could be the main reason that [email protected] enhances the reduction of Cd. The calculation results will help to explain the capture mechanism of Fe-modified biochar and guide materials design for Cd reduction in agricultural soils.

2. Results and Discussion

Firstly, the structural stability and electronic properties of graphene were considered with modified ferric hydroxide (Fe(OH)3) (Figure 1 and Figure S1). The optimization structures of G and [email protected] were compared. There was a long distance from Fe(OH)3 to G, which meant that a weak interaction existed between Fe(OH)3 and G (Figure 1a,b). Furthermore, the electron localization function (ELF) diagram proved that although the electron property of G changed with the Fe(OH)3 modification, there was no distinct electron exchange region between Fe(OH)3 and G that would demonstrate that a physical adsorption effect exists (Figure 1c,d). Meanwhile, these results implied that G would not have a negative influence on Fe(OH)3 to adsorb CdCl2.
To further explore the adsorption ability of CdCl2 on G and [email protected], the bond length (Cd-Cl), bond angle (Cl-Cd-Cl), and adsorption energy were considered. In previous studies, the long bond length and the large bond angle could facilitate the decomposition of the compound. Meanwhile, the weak adsorption energy could lead to the adsorption being unstable [29,30,31]. Compared with the pure CdCl2 (179.56°) and that adsorbed on G (171.03°), the CdCl2 showed the lowest bond angle (125.01°) when adsorbed on [email protected] (Figure 2a–c). Furthermore, in contrast to the pure CdCl2 and adsorbed on G, the [email protected] possessed a longer bond length (2.95Å, Cd-Cl) near the Fe(OH)3, whereas it had a shorter bond length (2.33Å, Cd-Cl) at the distance from Fe(OH)3. This was substantial evidence that CdCl2 would not decompose easily on [email protected] Moreover, adsorption energies of G and [email protected] with CdCl2 were taken for comparison. According to the computation formula of adsorption energy, the negative value implied a stronger restriction effect of CdCl2 adsorbed on substrates [32]. Due to the weak physisorption of G and CdCl2, G showed a poor adsorption ability (−0.42 eV), while [email protected] showed more negative values (−1.60 eV) when CdCl2 was adsorbed (Figure 2d). The above results demonstrated that with the introduction of Fe(OH)3, the [email protected] showed a considerable effect in restricting the migration of CdCl2.
Next, the electronic properties of CdCl2 on G and [email protected] were investigated to gain an understanding of the inhibition mechanism of CdCl2 on G and [email protected] Initially, the electron charge density difference of CdCl2 was drawn on G and [email protected] to probe the redistribution of charge. There was a clear charge depletion region between Cd and O atoms and a distinct charge accumulation region between Fe and Cl atoms, which indicated that a significant electron transfer occurred between the CdCl2 and [email protected] (Figure 3b,d). However, this phenomenon was only expressed between the CdCl2 and [email protected] interface. The adsorption configuration of CdCl2 on G was no evidence of an obvious charge transfer between Cd or Cl and G, which may be the main reason for the weak adsorption ability of CdCl2 on G (Figure 3a,c).
The above results are also observed in the ELF diagram (Figure 4). The CdCl2 on G configuration had no distinct electron exchange between the CdCl2 and G (Figure 4a). However, in contrast to G, the CdCl2 on [email protected] configuration had a greater electron redistribution than the ELF diagram of pure [email protected], where the localization degree of the electron for the -OH group near the Cd atom was reduced (Figure 4b,d). This phenomenon confirmed that CdCl2 had influenced the electronic properties of Fe(OH)3 in [email protected], which also implied that a significant charge exchange existed between Fe(OH)3 and CdCl2. Next, the Bader charge analysis method was used to gain a deeper insight into the number of charges transferred between substrates and CdCl2. Generally, more charges transferred expresses the higher restriction ability of the substrates to the molecules. Compared to the pure CdCl2, the Cd site of the CdCl2 on [email protected] configuration had an apparent charge transfer (0.141 e) that was higher than the CdCl2 on G configuration (0.008 e) (Figure 4c). In addition, as shown in Table S1, the two Cl atoms in the CdCl2 on [email protected] configuration also showed a charge exchange that was 0.05 e and 0.1 e greater than that of a Cl atom in pure CdCl2. The reason for the significant difference in charge number between the two Cl atoms was ascribed to the different distances from Fe(OH)3. Meanwhile, the total charge number of CdCl2 in the CdCl2 on [email protected] configuration showed a higher charge transfer than in other situations, and the results were consistent with Figure 3 and Figure 4.
The above data show that the formation of the Cd-O and Fe-Cl bonds benefitted from charges transferred between CdCl2 and the sorbent. However, in-depth studies must explore the reaction mechanism of CdCl2 adsorption on [email protected] Thus, the total density of states (DOS) and partial density of states (PDOS) of CdCl2 on G and [email protected] configurations were investigated to gain a perspective on the interval states of energy and electron transfer (Figure 5). Differing from the CdCl2 on G configuration (Figure 5a), there were prominent energy shifts that could be observed in the DOS of the CdCl2 on [email protected] configuration, which means that the electron transfer had occurred under the adsorption situation as displayed in Figure 5b. Furthermore, the PDOS of the O and Cd atoms in the CdCl2 on [email protected] configuration before and after adsorption were also considered. Due to the distinct charge donation of the Cd atom, the s-orbital of Cd exhibited a dramatic energy upshift after adsorption on [email protected] (Figure 5d). In contrast, the downshift of the p-orbital of O was evident, which was attributed to the O gain electrons when [email protected] interacted with CdCl2. Meanwhile, these phenomena were also present in the Fe s-orbital and Cl p-orbital of the CdCl2 on [email protected] configuration (Figure S2). However, there was no significant energy shift between the C p-orbital and Cd s-orbital of the CdCl2 on the G configuration (Figure 5c), which was consistent with the results of ELF, charge density difference, and Bader charge analysis.

3. Materials and Methods

The first principles calculations were carried out using the simulation software Vienna Ab initio Simulation Package (VASP) based on density functional theory (DFT) with the projector augmented wave (PAW) method [33,34,35]. Exchange-correction interactions were parameterized by the Perdew, Burke, and Ernzerhof (PBE) type, and DFT-D3 was used to consider the van der Waals interaction [36,37]. The energy cutoff was set to 500 eV, and convergence criteria for energy and force were set to 10−5 eV and 0.02 eV Å−1 per atom, respectively. A vacuum layer with a thickness of 15 Å was employed to avoid interactions between the adjacent periodic units. The k-point was meshed by the Monkhorst–Pack method with a 3 × 3 × 1 grid for geometry optimizations and 11 × 11 × 1 grid for DOS calculation [38,39]. The calculations were computed within the DFT + U formalism to describe the localized d electrons, and the U values of Fe and Cd were set to 4 eV and 2 eV, respectively [40,41]. The adsorption energy (Ea) formula was defined as
Ea = E(Cd-substrate) − (ECd + Esubstrate),
where ECd, Esubstrate, and E(Cd-substrate) represent the total energy of the CdCl2, the substrates of G or [email protected], and the energy of the CdCl2 adsorption on the different substrates. The differential charge density (Δρ) that was used to describe the charge distribution for the adsorption system is defined with the following formula [42]:
Δρ = ρCd-substrate − ρsubstrate − ρCd,
where ρCd-substrate, ρsubstrate, and ρCd represent the charge density of the CdCl2 adsorption on the different substrates, the substrates of G or [email protected], and the CdCl2. The electron localization function (ELF) diagram was drawn by VESTA [43].

4. Conclusions

In summary, we have revealed the capture ability and mechanism of CdCl2 with Fe(OH)3 modified graphene via first principles calculations. The Fe(OH)3 modified carbon did not have a negative influence on adsorption of CdCl2, and it could increase the chemisorption effect when the Fe(OH)3 was introduced. This led to an adsorption energy improvement from −0.42 eV (G) to −1.60 eV. The adsorption behavior of [email protected] would then result in a large change in bond length (Cd-Cl) and bond angle (Cl-Cd-Cl) when CdCl2 was adsorbed onto [email protected] Furthermore, the electron charge density difference, ELF, and Bader charge analysis were used to confirm the charge transfer capacity. The Bader charge analysis displayed a 0.141 e charge transfer between Cd and [email protected], which showed a greater amelioration over the CdCl2 on G configuration. In addition, the electron transfer process was revealed by DOS and PDOS analysis. The PDOS proved that the Cd s-orbital and the O p-orbital exhibited a dramatic energy shift when the [email protected] interacted with CdCl2, which provided powerful evidence for the capture mechanism of CdCl2 with Fe(OH)3 modified carbon. This study identified a powerful adsorption material for Cd reduction in agricultural soils and revealed the capture mechanism of [email protected] for Cd addition, showing potential as a strategy for Cd reduction in agricultural soils.

Supplementary Materials

The following supporting information can be downloaded at:, Figure S1: ELF diagram of the top view of [email protected]; Figure S2: The partial density of states of CdCl2 adsorbed on [email protected]; Table S1: The number of charge transfers of the pure CdCl2, and adsorbed on substrate.

Author Contributions

X.W., J.D. and Z.F.: conception and design of the study, approval of the version of the manuscript to be published; H.W. performed the study, analyzed the data, and wrote the manuscript; J.H., W.Z. and P.L. provided guidance on the data analysis; Y.W., F.Z. and X.M. revised the manuscript critically for important intellectual content. All authors have read and agreed to the published version of the manuscript.


This study is supported by the National Natural Science Foundation of China (Grant No. 31501277).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.


We thank the Agriculture and Rural Affairs Department of Hunan Province for their support of the research and demonstration of a high-efficiency rice model and disaster avoidance technology and the project of Breeding and Application of Rice Varieties with Low Cadmium Accumulation.

Conflicts of Interest

The authors declare no conflict of interest.


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Figure 1. Schematic of G (a) and [email protected] (b), ELF diagram of G (c) and [email protected] (d).
Figure 1. Schematic of G (a) and [email protected] (b), ELF diagram of G (c) and [email protected] (d).
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Figure 2. Schematic of pure CdCl2 (a), CdCl2 on G (b) and on [email protected] (c). (d) Adsorption energies of CdCl2 on G and [email protected]
Figure 2. Schematic of pure CdCl2 (a), CdCl2 on G (b) and on [email protected] (c). (d) Adsorption energies of CdCl2 on G and [email protected]
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Figure 3. Charge density difference of the front views of CdCl2 on G (a) and [email protected] (b), and the top views of CdCl2 on G (c) and [email protected] (d). The isosurface is set to 3 × 10−4 e Å−3 in CdCl2 on G and set to 3 × 10−3 e Å−3 in CdCl2 on [email protected] Note that yellow and red correspond to charge depletion and charge accumulation.
Figure 3. Charge density difference of the front views of CdCl2 on G (a) and [email protected] (b), and the top views of CdCl2 on G (c) and [email protected] (d). The isosurface is set to 3 × 10−4 e Å−3 in CdCl2 on G and set to 3 × 10−3 e Å−3 in CdCl2 on [email protected] Note that yellow and red correspond to charge depletion and charge accumulation.
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Figure 4. ELF diagram of CdCl2 on G (a) and [email protected] (b). (c) The number of charge transfers of the Cd site for the CdCl2 on substrates. Note that the dark and light green regions correspond to the number of electrons of the Cd for the CdCl2 after adsorption on substrates, and the difference value with the electrons of the Cd for the pure CdCl2, respectively. ELF diagram of top view of CdCl2 on [email protected] (d).
Figure 4. ELF diagram of CdCl2 on G (a) and [email protected] (b). (c) The number of charge transfers of the Cd site for the CdCl2 on substrates. Note that the dark and light green regions correspond to the number of electrons of the Cd for the CdCl2 after adsorption on substrates, and the difference value with the electrons of the Cd for the pure CdCl2, respectively. ELF diagram of top view of CdCl2 on [email protected] (d).
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Figure 5. The density of states of CdCl2 adsorbed on G (a) and [email protected] (b). The partial density of states of CdCl2 adsorbed on G (c) and [email protected] (d).
Figure 5. The density of states of CdCl2 adsorbed on G (a) and [email protected] (b). The partial density of states of CdCl2 adsorbed on G (c) and [email protected] (d).
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