Context Toxic agents in the environment represent a serious threat to human life and pose a major problem, which has led scientists to conduct continuous research into methods for detecting and removing them from the environment. For example, H₂S, SO₂, NH₃, CO, CO₂, NO, and NO₂ are toxic agents commonly found in their gaseous state. Enhancing environmental sensing is, therefore, essential for protecting the ecosystem. In this context, we suggest new complexes of copper and cobalt based on thymine base pair: [thym-Co-thym] and [thym-Cu-thym] as sensors to detect and to attract toxic agents. Our theoretical study demonstrates the potential of the proposed complexes to act as biosensors capable of capturing toxic agents from the environment, as supported by various quantum chemistry methods, including quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), natural bond orbitals (NBO), and non-covalent interaction (NCI) analysis. Orbital interaction is favored for H2S (0.06 eV, 0.04 eV) and NO (0.24 eV, 0.35 eV) for both complexes [thym-Co-thym] and [thym-Cu-thym] respectively. Energetically, interaction of [thym-Co-thym] and [thym-Cu-thym] is more favorable with SO2 (− 319.9 kcal/mol, − 332.5 kcal/mol respectively) than with the other agents. According to the RDG (reduced density gradient) method, the values of (signλ2) ρ(r) where λ2 is the second eigenvalue of the electron density Hessian matrix, are negative with ρ(r) > 0. This indicates strong attractive non-covalent interactions such as hydrogen bonding and halogen bonding between the complexes and the toxic agents, case of HCN with thym-Cu-thym and NO with thym-Co-thym. Most of the other interactions between the complexes and the toxic agents are of the van der Waals type, as (sign λ2) ρ(r)≈0. The quantum theory of atoms in molecules (QTAIM) confirms the interactions between the proposed complexes and the toxic agents through the appearance of bond critical points (BCPs). The topological analysis of the Laplacian of the electron density <InlineEquation ID="IEq1"> <EquationSource Format="TEX">${\nabla }^{2}$</EquationSource> <EquationSource Format="MATHML"><math> <msup> <mrow> <mi mathvariant="normal">∇</mi> </mrow> <mn>2</mn> </msup> </math></EquationSource> </InlineEquation> ρ(r), the electron density ρ(r), and the total electronic energy density H(r) at these BCPs indicates that the interactions between the complexes and the toxic agents are predominantly classified as pure closed-shell interactions, except in the case of NO and NO₂, which exhibit partial covalent character with both cobalt and copper complexes. Quantum theory of atoms in molecules is in accord with reduced density gradient (RDG) in description of non-covalent interactions. All these factors could support the environmentally sustainable synthesis of these molecules as biosensors. Interaction of the two complexes with adducts increases the hardness (η) values. Softness decreases after interaction with adducts. The electronegativity (χ) and electrophilicity (ω) are decreased after interacting with adducts, so that the ability to capture one or more electrons will be reduced. Most of donor–acceptor orbitals fortify the interaction of different adducts with both of [thym-Co-thym] and [thym-Cu-thym] complexes. [thym-Co-thym] complex exhibits best detection of NO2 and NO by a broad rise at 400–500 nm and of SO2 through an intensity jump blue-shift in the UV, while [thym-Cu-thym] complex detects H2S and HCN by strong band at almost 470–500 nm. CO2 is weakly interacting in both complexes. At 200–400 nm region [thym-Co-thym] shows well detection of SO2, H2S, CO2, CO, and HCN, whereas [thym-Cu-thym] indicates well detection of NO, CO, CO2, H2S, and SO2. Methods Studied structures are optimized at DFT/M06-2x/6–311 + G(d,p) level of theory implemented in Gaussian16. The pseudopotential LanL2DZ is used for metals copper and cobalt. [thym-Cu-thym] and [thym-Co-thym] complexes are reoptimized toward considered species and in the presence of humidity (H2O molecule) at the same level of theory. Relativistic effects are taken through the fourth-(DKH4) and zeroth-order Douglas–Kroll–Hess (DKH0) approximations applying cc-pVDZ-DK basis set, spin–orbit effects are taken into account through DKHSO. Frequency calculations give real frequencies confirming the stability of the two complexes and ensure that the structures correspond to the lowest potential energy. Natural bond orbital (NBO) was performed at the same way using the version implemented in Gaussian16. All optimized structures were analyzed using VMD (visual molecular dynamics). The reduced density gradient (RDG) method was applied, and the function sign(λ₂)ρ(r) was requested to identify the type of non-covalent interaction between the complexes and the adducts (toxic agents). RDG scatter plots are drawn by multiwfn program and colored using gnuplot for improved visualization. Furthermore, the quantum theory of atoms in molecules (QTAIM) analysis confirmed the non-covalent interactions between complexes and adducts (toxic agents). UV–Vis absorption spectra of the all studied complexes were obtained by TD-DFT at the same level of theory TD-SCF/ M602x/6-311G** level of theory.

New sensors based on DNA base pairs: DFT, QTAIM, and NCI-RDG study

期刊论文
发表日期：

2025年11月11日

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Mona Boudiaf,
Nour Elyakine Amraoui,
Henry Chermette

摘要

Context

Toxic agents in the environment represent a serious threat to human life and pose a major problem, which has led scientists to conduct continuous research into methods for detecting and removing them from the environment. For example, H₂S, SO₂, NH₃, CO, CO₂, NO, and NO₂ are toxic agents commonly found in their gaseous state. Enhancing environmental sensing is, therefore, essential for protecting the ecosystem. In this context, we suggest new complexes of copper and cobalt based on thymine base pair: [thym-Co-thym] and [thym-Cu-thym] as sensors to detect and to attract toxic agents. Our theoretical study demonstrates the potential of the proposed complexes to act as biosensors capable of capturing toxic agents from the environment, as supported by various quantum chemistry methods, including quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), natural bond orbitals (NBO), and non-covalent interaction (NCI) analysis. Orbital interaction is favored for H₂S (0.06 eV, 0.04 eV) and NO (0.24 eV, 0.35 eV) for both complexes [thym-Co-thym] and [thym-Cu-thym] respectively. Energetically, interaction of [thym-Co-thym] and [thym-Cu-thym] is more favorable with SO₂ (− 319.9 kcal/mol, − 332.5 kcal/mol respectively) than with the other agents. According to the RDG (reduced density gradient) method, the values of (signλ2) ρ(r) where λ2 is the second eigenvalue of the electron density Hessian matrix, are negative with ρ(r) > 0. This indicates strong attractive non-covalent interactions such as hydrogen bonding and halogen bonding between the complexes and the toxic agents, case of HCN with thym-Cu-thym and NO with thym-Co-thym. Most of the other interactions between the complexes and the toxic agents are of the van der Waals type, as (sign λ2) ρ(r)≈0. The quantum theory of atoms in molecules (QTAIM) confirms the interactions between the proposed complexes and the toxic agents through the appearance of bond critical points (BCPs). The topological analysis of the Laplacian of the electron density ${\nabla }^{2}$ $\nabla^{2}$ ρ(r), the electron density ρ(r), and the total electronic energy density H(r) at these BCPs indicates that the interactions between the complexes and the toxic agents are predominantly classified as pure closed-shell interactions, except in the case of NO and NO₂, which exhibit partial covalent character with both cobalt and copper complexes. Quantum theory of atoms in molecules is in accord with reduced density gradient (RDG) in description of non-covalent interactions. All these factors could support the environmentally sustainable synthesis of these molecules as biosensors. Interaction of the two complexes with adducts increases the hardness (η) values. Softness decreases after interaction with adducts. The electronegativity (χ) and electrophilicity (ω) are decreased after interacting with adducts, so that the ability to capture one or more electrons will be reduced. Most of donor–acceptor orbitals fortify the interaction of different adducts with both of [thym-Co-thym] and [thym-Cu-thym] complexes. [thym-Co-thym] complex exhibits best detection of NO₂ and NO by a broad rise at 400–500 nm and of SO₂ through an intensity jump blue-shift in the UV, while [thym-Cu-thym] complex detects H₂S and HCN by strong band at almost 470–500 nm. CO₂ is weakly interacting in both complexes. At 200–400 nm region [thym-Co-thym] shows well detection of SO₂, H₂S, CO₂, CO, and HCN, whereas [thym-Cu-thym] indicates well detection of NO, CO, CO₂, H₂S, and SO₂.

Methods

Studied structures are optimized at DFT/M06-2x/6–311 + G(d,p) level of theory implemented in Gaussian16. The pseudopotential LanL2DZ is used for metals copper and cobalt. [thym-Cu-thym] and [thym-Co-thym] complexes are reoptimized toward considered species and in the presence of humidity (H₂O molecule) at the same level of theory. Relativistic effects are taken through the fourth-(DKH4) and zeroth-order Douglas–Kroll–Hess (DKH0) approximations applying cc-pVDZ-DK basis set, spin–orbit effects are taken into account through DKHSO. Frequency calculations give real frequencies confirming the stability of the two complexes and ensure that the structures correspond to the lowest potential energy. Natural bond orbital (NBO) was performed at the same way using the version implemented in Gaussian16. All optimized structures were analyzed using VMD (visual molecular dynamics). The reduced density gradient (RDG) method was applied, and the function sign(λ₂)ρ(r) was requested to identify the type of non-covalent interaction between the complexes and the adducts (toxic agents). RDG scatter plots are drawn by multiwfn program and colored using gnuplot for improved visualization. Furthermore, the quantum theory of atoms in molecules (QTAIM) analysis confirmed the non-covalent interactions between complexes and adducts (toxic agents). UV–Vis absorption spectra of the all studied complexes were obtained by TD-DFT at the same level of theory TD-SCF/ M602x/6-311G** level of theory.