Introduction

While most polymers are typically insulators, some are considered conducting polymers, which are comparable in their properties to those of inorganic semiconductors and metals1,2. Those classes of conducting polymers show single and double bonds in the conjugated carbon chain, which create highly nonlocal, polarized, electron-dense π bonds responsible for their unique electrical and optical properties3. Polypyrrole (PPy), among other conducting polymers show stable structure, conductive easy forming composites, beside electrochemical activity, which dedicate it for sensing applications4,5. The deep need for sensors operating at room temperature derive the root toward conducting polymers6. In this sense, polymer composites, especially nanocomposite could be the solution for room temperature sensors. These polymers show interesting electronic as well as electrochemical properties7. Such class of composites is promising based on their enhanced optical, electronic and mechanical properties8. Graphene oxide GrO is a 2D hexagonal lattice carbon material that finds ways to different applications owing to its optical and electronic properties9. The promising applications of such carbon-based material are due to their high charge carrier mobility, and mechanical qualities10. Graphene oxide enhances the optical and band gap energy of PPy as they form composite together11.

As stated earlier that the PPys π-electron-rich endows it with a pronounced affinity for specific metal ions, facilitating interactions characterized by electrostatic attraction and coordination. The inherent conductivity of PPy is further harnessed to enhance its capabilities in electrochemical sensing applications12,13. The functionalization of polymers involves modifying their chemical structures to increase properties such as solubility, adhesion, and reactivity, which is necessary to tailor their properties to specific applications, improve their performance, and extend their usability14,15. Amino-functionalized graphene oxide/polypyrrole (AM-GrO/PPy) composite-based novel sensing platform was established to monitor lead ions (Pb2+) at high sensitivity16. It was stated that, the AM-GrO/PPy composite emerges as efficient sensor acts for the electrochemical detection of Pb2+, holding significant potential for environmental monitoring and the protection of human health. The PPy-GrO composite is also presented as a promising material and a sensor device developed using interdigitated copper electrode on copper clad is a cost-effective approach for detection of CO17. Development of cost effective and selective gas sensor is a hot topic of research18. Molecular modeling is a class of computational work elucidating the electronic, physical and chemical properties of a wide range of molecular systems19,20.

Molecular modeling was used to study PLA/GrO/ZnO and PLA/GrO/Cu2O interacting with gases and volatile organic compounds. Results indicated that these composites could be used as gas sensors21. A study based on computational molecular modeling indicated that the graphene oxide/WO3/polyvinylidene fluoride composite could be applied as biosensor22. It is stated that molecular modeling introduced important computational data that supports the experimental findings. This data was able to describe the mechanism of interaction between the nanocomposite surface and the studied gases23,24,25.

DFT has been used to study the interaction of cysteine with boron nitride nanotubes, which could lead to the development of new nano sensors and nano carriers for this and other amino acids26. In biomedical applications, DFT has also been used to identify hybrid B12N12/ZIF-8 nanoclusters as a potential platform for sensing the drug AMP. A detailed DFT analysis of their adsorption behavior, electronic properties, and intermolecular interactions showed their potential to effectively bind to and detect the drug27. Furthermore, DFT allows researchers to track key parameters like QTAIM and NCI to study the adsorption of organic structures on nanomaterials28.

In this work, a ternary nanocomposite comprising graphene oxide (GrO), polypyrrole (PPy), and zinc oxide (ZnO) is computationally designed and characterized to evaluate its potential for alanine sensing. The study focuses on elucidating how surface functionalization with amino (NH₂) and carboxyl (COOH) groups modulates the composite’s electronic and reactive properties. A comprehensive set of computational analyses is performed, including total dipole moment (TDM), HOMO–LUMO energy gap, Quantum Theory of Atoms in Molecules (QTAIM) analysis, molecular electrostatic potential (MESP) mapping, and global reactivity descriptors. Additionally, Non-Covalent Interaction (NCI) and Reduced Density Gradient (RDG) analyses are employed to prove weak intermolecular interactions between alanine and the functionalized composites. Density Functional Theory (DFT) calculations are used to determine ionization potential, electron affinity, chemical hardness, absolute softness, electronic chemical potential, and electrophilicity index, enabling quantitative assessment of changes upon alanine binding. The ultimate objective is to compare the sensing performance of NH₂- and COOH-functionalized systems, establish correlations between electronic structure modulation and selective analyte recognition, and identify the functionalization strategy that achieves the optimal balance of sensitivity, selectivity, and structural stability for high-performance amino acid detection.

Computational details

The model system investigated in this study comprises alanine, graphene oxide (GrO), polypyrrole (PPy), and zinc oxide (ZnO).

Figure 1a shows the optimized structure of alanine, selected as a minimal amino acid model due to its two key functional groups, the amino group (NH₂) and the carboxyl group (COOH), which act as primary hydrogen-bonding sites and dominate amino acid–surface interactions. Alanine was chosen for three reasons: (i) computationally, it is the simplest chiral amino acid containing both NH₂ and COOH moieties, enabling clear mechanistic interpretation at reduced computational cost; (ii) biologically, its plasma concentration is a clinically relevant biomarker for liver function, metabolic disorders, and muscle health; and (iii) mechanistically, its interaction via amino and carboxyl groups is representative of most amino acids, thereby supporting generalization of the results to broader sensing applications. Importantly, these two universal functional groups are the principal determinants of amino acid binding to nanomaterials through hydrogen bonding, electrostatics, and coordination interactions. Hence, the interaction mechanisms observed in this study capture the fundamental binding motifs common across the amino acid family. This methodological approach has been widely adopted in both computational and experimental investigations, where alanine serves as a model probe for generalizing amino acid adsorption and sensing behavior on nanostructured surfaces29. While side-chain variations may introduce secondary effects (e.g., hydrophobic or aromatic interactions), the dominant NH₂/COOH-driven interactions captured by our alanine model provide a robust foundation for extrapolating the findings to other amino acids.

Figure 1b presents the GrO model, represented as a two-dimensional nanostructure functionalized with hydroxyl (OH) and carboxyl (COOH) groups. These oxygen-containing functionalities are distributed across the surface, enabling interactions through surface coordination rather than chain-length effects. Figure 1c shows the PPy model composed of three repeating pyrrole units, and Fig. 1d provides the atomic site labeling for reference.

Figure 2a depicts the binary GrO/PPy composite, while Fig. 2b illustrates the ternary GrO/PPy/ZnO system obtained by incorporating ZnO nanoparticles. The choice of GrO, ZnO, and a three-unit PPy chain achieves a balance between computational tractability and accuracy. Comparable model sizes have been shown to capture essential physicochemical interactions and reproduce interfacial properties observed in larger systems, thereby enabling accurate predictions without prohibitive computational demands.

The interaction of alanine with the ternary composite was examined in two configurations: (i) through the amino group (GrO/PPy/ZnO/NH₂), as shown in Fig. 2c, and (ii) via the carboxyl group (GrO/PPy/ZnO/COOH), as shown in Fig. 2d.

All calculations were carried out using the Gaussian 09 (G09) software package30, running on a personal workstation at the Molecular Modeling and Spectroscopy Laboratory, Centre of Excellence for Advanced Science, National Research Centre, Egypt. Geometry optimizations were performed using density functional theory (DFT) at the B3LYP level of theory, employing Becke’s three parameter exchange functional combined with the Lee-Yang-Parr correlation functional31,32,33. The Los Alamos National Laboratory 2 Double-Zeta (LANL2DZ) basis set was applied, suitable for systems containing transition metals such as zinc34.

This choice ensured reliable treatment of Zn while maintaining computational feasibility for the full nanocomposite. Although no additional benchmarking with larger split-valence basis sets was performed for the organic components, LANL2DZ has been widely applied in similar hybrid systems, and the consistency of our descriptors (ΔE, TDM, QTAIM, NCI) supports the reliability of the obtained results. Benchmarking with mixed basis sets (e.g., 6-31G for light atoms) will be considered in future work to further refine accuracy. Optimizations proceeded until all convergence criteria were satisfied, including thresholds for the maximum force, root mean square (RMS) force, maximum displacement, and RMS displacement. The calculated change in total energy ranged from − 9.819654D-09 to -1.441622D-08 Hartree, indicating successful convergence and energy minimization of the model systems.

In addition to geometry optimization, a range of theoretical properties and molecular descriptors was calculated, including total dipole moment (TDM), HOMO–LUMO energy gap (ΔE), and global reactivity descriptors [ionization potential (I), electron affinity (A), chemical hardness (η), absolute softness (S), electronic chemical potential (µ), electrophilicity index (ω), and electronegativity (χ)]. Bond topology and hydrogen-bonding interactions were analyzed using Quantum Theory of Atoms in Molecules (QTAIM), while molecular electrostatic potential (MESP) mapping was employed to visualize charge distribution and reactive sites. Non-covalent interaction (NCI) and reduced density gradient (RDG) analyses were performed to characterize weak intermolecular forces such as hydrogen bonding, π–π stacking and van der Waals interactions. Density of states (DOS) calculations were also carried out to examine modifications in the electronic structure upon composite formation and alanine functionalization.

Fig. 1
figure 1

Optimized model structures of the individual components used in the study: (a) Alanine; (b) Graphene oxide (GrO); (c) Polypyrrole (PPy); (d) Labeled atomic sites for identification within the studied molecules.

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Fig. 2
figure 2

Optimized model structures of the composite and interaction systems: (a) GrO/PPy binary composite; (b) GrO/PPy/ZnO ternary nanocomposite; (c) GrO/PPy/ZnO/NH₂ complex interacting via the amino group of alanine; (d) GrO/PPy/ZnO/COOH complex interacting via the carboxyl group of alanine.

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Results and discussion

Physical parameters

Density Functional Theory (DFT) calculations of physical parameters provide key insights into the electronic structure, polarity, and potential reactivity of nanocomposite materials. Among these descriptors, the total dipole moment (TDM) and the HOMO–LUMO energy gap (ΔE) are widely recognized as indicators of molecular reactivity and intermolecular interaction potential35,36. In general, an increase in TDM accompanied by a decrease in ΔE reflects greater polarity, enhanced electronic delocalization, and higher susceptibility to chemical interaction.

The calculated TDM and ΔE values for all studied systems are presented in Table 1. Pristine graphene oxide (GrO) and polypyrrole (PPy) exhibited relatively low dipole moments (1.99 D and 2.19 D, respectively) and moderate electronic gaps (2.70 eV for GrO and 4.26 eV for PPy). Upon formation of the GrO/PPy composite, the TDM increased substantially to 5.71 D, indicating enhanced polarity and the emergence of additional potential binding sites. This increase was accompanied by a sharp reduction in the energy gap to 1.36 eV, signifying increased electronic delocalization and potential reactivity.

Incorporating ZnO into the composite produced only a slight decrease in TDM (5.62 Debye) and a modest increase in ΔE (1.64 eV), suggesting that ZnO slightly moderates the polarity without significantly altering the electronic delocalization of the hybrid structure.

To explore interactions with biomolecules, alanine was selected as a model amino acid, representing common protein functional groups. Two binding orientations were investigated: via the carboxylic acid (COOH) group and via the amino (NH₂) group. Upon binding, the TDM values decreased notably to 2.81 Debye (COOH-bound) and 2.77 Debye (NH₂-bound), while ΔE increased to 2.20 eV and 2.08 eV, respectively. These changes suggest that alanine binding reduces the overall polarity and reactivity of the composite, likely due to stabilization through hydrogen bonding, coordination interactions, and charge redistribution. The slightly higher ΔE observed for the COOH-bound system implies a marginally more stabilized and less reactive configuration compared to the NH₂-bound counterpart.

Table 1 Calculated total dipole moments (TDM, Debye) and HOMO–LUMO band gap energies (ΔE, eV) at the B3LYP/LANL2DZ level of theory.
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Quantum theory of atoms in molecules (QTAIM)

The Quantum Theory of Atoms in Molecules (QTAIM) provides a rigorous quantum mechanical framework for analyzing the topology of electron density within molecular systems. By identifying critical points-bond critical points (BCPs), ring critical points (RCPs), and nuclear critical points (NCPs)-along with the bond paths connecting them, QTAIM enables detailed characterization of both covalent and non-covalent interactions, including hydrogen bonding, van der Waals forces, and coordination bonds. This method offers valuable insight into molecular stability, reactivity, and electronic delocalization phenomena that govern intermolecular interactions37,38,39.

For the unmodified GrO/PPy composite (Fig. 3a), QTAIM descriptors reveal strong covalent C–C and C–N bonds (ρ(r) > 0.25 e/ų, H(r) < 0) and moderate closed-shell hydrogen bonds at O–H···O contacts, indicative of a stable covalent framework reinforced by interfacial hydrogen bonding.

Upon ZnO incorporation (Fig. 3b), new Zn–O coordination bonds (ρ(r) ≈ 0.05–0.07 e/ų, ∇²ρ > 0) emerge in addition to the existing covalent and hydrogen-bond networks. These coordination interactions potentially enhance electronic coupling and increase surface reactivity.

The QTAIM parameters for the alanine-functionalized composites (Tables 1 and 2) reveal distinct binding characteristics for the two functional groups. In the NH₂-bound system (Fig. 3c; Table 1), multiple Zn–N and Zn–O coordination bonds coexist with strong hydrogen bonds (ρ(r) ≈ 0.022–0.025 e/ų, positive ∇²ρ), forming a flexible interaction network. Elevated ellipticity values for certain BCPs suggest adaptable binding geometries, which may favor versatile molecular recognition. In contrast, the COOH-bound system (Fig. 3d; Table 2) contains fewer but stronger Zn–O coordination and O–H···O hydrogen bonds, resulting in a more localized and rigid binding configuration. This rigidity may improve selectivity but could reduce the diversity of possible interactions. The QTAIM topological parameters for the GrO/PPy/ZnO/COOH composite were listed in Table 3. The table lists the bond critical point (BCP) indices, bond types, electron density ρ(r), kinetic energy density G(r), potential energy density V(r), total energy density H(r), Laplacian of electron density ∇²ρ(r), and ellipticity (ε). Interaction types are classified according to QTAIM criteria into covalent, coordination, hydrogen-bond, van der Waals, and weak covalent interactions.

Fig. 3
figure 3

QTAIM calculated for the studied structures whereas; a- GrO/PPy, b- GrO/PPy/ZnO, c- GrO/PPy/ZnO/NH2, and d- GrO/PPy/ZnO/COOH.

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Table 2 QTAIM topological parameters for the GrO/PPy/ZnO/NH2 composite.
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Table 3 QTAIM topological parameters for the GrO/PPy/ZnO/COOH composite.
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Molecular electrostatic potential (MESP)

The molecular electrostatic potential (MESP) maps of the studied systems (Fig. 4) provide insight into surface charge distribution and the locations most favorable for alanine interaction.

The unmodified GrO/PPy composite (Fig. 4a) shows a balanced distribution of electron-rich (blue) and electron-deficient (red/yellow) regions, indicating a baseline electrostatic profile with moderate polarity. Incorporation of ZnO (Fig. 4b) increases the heterogeneity of the electrostatic potential, particularly at the interface regions, creating additional polar sites that can serve as potential binding points for alanine.

When alanine is bound through its NH₂ group (Fig. 4c), the composite surface displays an enhanced positive potential near the amine binding site, reflecting stronger hydrogen-bond donor capability toward electron-rich regions of the alanine molecule. In contrast, when alanine is bound via its COOH group (Fig. 4d), the MESP reveals pronounced dipolar features around the carboxylate binding region, suggesting an increased ability to interact with polar or hydrogen-bond-accepting regions on the composite.

These differences indicate that NH₂ binding promotes a more flexible interaction profile, whereas COOH binding results in a more localized, high-polarity binding environment. Such variation in electrostatic surface characteristics may influence the sensitivity and selectivity of GrO–PPy–ZnO toward alanine detection.

Fig. 4
figure 4

MESP calculated for the studied structures whereas; a- GrO/PPy, b- GrO/PPy/ZnO, c- GrO/PPy/ZnO/NH2, and d- GrO/PPy/ZnO/COOH.

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Global reactivity descriptors

Global reactivity descriptors quantitatively describe molecular reactivity and electronic properties, providing key insights into chemical behavior and sensor performance. The ionization potential (I), electron affinity (A), electronic chemical potential (µ), chemical hardness (η), absolute softness (S), and electrophilicity index (ω) were calculated from frontier molecular orbital energies (HOMO and LUMO) according to established equations40: I = − EHOMO, A = − ELUMO, µ = −(I + A)/2, η = (I − A)/2, S = 1/η, and ω = µ²/2η.

Table 4 presents the B3LYP/LANL2DZ-calculated descriptors for pristine GrO, PPy, the GrO/PPy/ZnO composite, and its COOH- and NH₂-functionalized derivatives upon interaction with alanine.

The pristine GrO/PPy/ZnO composite shows an ionization potential of 3.03 eV, which decreases to 2.56 eV for the COOH-functionalized system and 2.67 eV for the NH₂-functionalized variant after alanine binding. This reduction indicates greater ease of electron removal, enhancing electronic accessibility at the sensor surface. Concurrently, electron affinity increases in both functionalized systems, signifying an improved electron-accepting capability and promoting charge transfer processes critical for sensing.

Chemical hardness (η) and absolute softness (S) change modestly after binding, suggesting slight adjustments in structural flexibility without compromising stability. Notably, electrophilicity index (ω) and electronegativity (χ) decrease upon alanine interaction, implying reduced electron-withdrawing tendency, which can paradoxically favor selective recognition by lowering the energy barrier for analyte–sensor interaction.

Overall, the COOH-functionalized composite demonstrates the most favorable combination of low ionization potential and high electron affinity, producing an electronic environment well-suited for selective alanine detection. These correlations between global reactivity descriptors and binding behavior support the potential of functionalized GrO/PPy/ZnO as a high-performance chemical sensor41.

Table 4 B3LYP/LANL2DZ-calculated global reactivity descriptors for studied structures.
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Density of States DOS

The density of states (DOS) is calculated also at B3LYP/LANL2DZ and plotted with the help of Gauss sum program41. The DOS describes the number of allowed modes or states per unit energy range. Figure 5 illustrates the DOS for the interactions of GrO with PPy, as well as with ZnO through the COOH and NH2 functional groups. As indicated in Fig. 5a and c, both alanine and PPy exhibit the largest energy band gaps. In contrast, GrO demonstrates a considerably smaller energy gap, as shown in Fig. 5b. This phenomenon can be explained by the electronic structure of graphene oxide, which typically features a reduced band gap due to its sp² hybridized carbon atoms and the presence of oxygen-containing functional groups. When GrO interacts with PPy, or when ZnO is involved with GrO/PPy, there is a significant decrease in the energy band gap, as illustrated in Fig. 5d and e, respectively. This reduction is likely a result of the synergistic interaction between ZnO and GrO/PPy, where ZnO may either donate or accept electrons, thereby modifying the electronic characteristics of the composite material. Such interactions lead to a shift in energy levels, which diminishes the band gap and enhances charge transfer capabilities.

The Density of States (DOS) analysis shows changes in the band gap upon interaction. Furthermore, the energy gap also diminishes when interactions occur via the COOH group, as shown in Fig. 5f, and similarly when the NH2 group is involved, as depicted in Fig. 5g. These findings indicate that the COOH and NH2 functional groups significantly influence the electronic structure and promote electron transfer. The most pronounced alteration in the DOS and the lowest energy gap are observed in the GrO/PPy/ZnO composite, as emphasized in the figures. This observation aligns with the calculated energy gap, suggesting that the combination of GrO, PPy, and ZnO leads to an optimized electronic structure, thereby enhancing the overall electronic properties of the material. This composite is particularly advantageous for applications requiring efficient charge transport, such as in sensors, energy storage systems, or catalysis.

Fig. 5
figure 5

Density of states for the studied structures whereas; a- Alanine, b- Graphene oxide (GrO), c- Polypyrrole (PPy); d- GrO/PPy, e- GrO/PPy/ZnO, f- GrO/PPy/ZnO/COOH, and g- GrO/PPy/ZnO/NH2.

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Non-Covalent interactions (NCI) and reduced density gradient (RDG) analysis

Non-covalent interaction (NCI) and reduced density gradient (RDG) analyses were performed to systematically investigate weak intermolecular interactions within the studied nanocomposite systems. These complementary computational methods, visualized through distinct color-coded isosurfaces42, provide comprehensive insights into hydrogen bonding networks, van der Waals forces, and steric repulsion effects. The NCI visualization scheme employs a standardized color mapping where red isosurfaces indicate strong repulsive interactions, blue regions represent strong attractive interactions, and green areas correspond to weaker interactions such as van der Waals or dispersion forces. Non-covalent interaction (NCI) and reduced density gradient (RDG) analyses complement QTAIM by visualizing weak interaction domains via color-coded isosurfaces. In the pristine GrO–PPy composite (Fig. 6a, b), extended green isosurfaces dominate the interfacial regions, consistent with π–π stacking and van der Waals dispersion between the polypyrrole and graphene oxide layers. Localized blue areas coincide with hydrogen-bond sites, reinforcing QTAIM findings.

ZnO incorporation (Fig. 6c, d) introduces pronounced blue domains near Zn–O coordination points, signifying strong attractive forces, and a wider spread of green regions along the GrO–ZnO and PPy–ZnO boundaries, indicative of enhanced dispersion stabilization. This expansion of interaction domains implies a more heterogeneous and adsorption-friendly surface.

For the alanine-bound systems, the NH₂-functionalized composite (Fig. 6e, f) shows a broad distribution of green zones interspersed with blue coordination sites, pointing to synergistic effects between dispersion forces and metal–ligand coordination. The COOH-bound composite (Fig. 6g, h) displays more concentrated blue regions, corresponding to fewer but stronger hydrogen bonds and coordination interactions. This spatial distribution supports the QTAIM observation of a more rigid binding environment, which may be beneficial for selective molecular recognition.

Fig. 6
figure 6

NCI (a, c, e, g) and RDG (b, d, f, h) calculated for the studied structures: a/b - GrO/PPy, c/d - GrO/PPy/ZnO, e/f - GrO/PPy/ZnO/NH2, and g/h - GrO/PPy/ZnO/COOH.

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Conclusion

This computational investigation provides a comprehensive understanding of the electronic and interactional characteristics of a graphene oxide–polypyrrole–zinc oxide (GrO/PPy/ZnO) nanocomposite and its NH₂- and COOH-functionalized derivatives for alanine sensing. The pristine composite exhibits an ionization potential (I) of 3.03 eV and an electron affinity (A) of 4.68 eV, supporting balanced electron-donating and electron-accepting abilities. Upon alanine binding, COOH functionalization yields the most pronounced changes, reducing I from 3.03 eV to 2.56 eV and increasing A from 4.68 eV to 4.77 eV, creating an electronic environment highly favorable for charge-transfer-driven sensing. NH₂ functionalization also enhances reactivity, lowering I to 2.67 eV and raising A to 4.75 eV, but with a smaller effect than COOH. Variations in chemical hardness (η) remain modest (from − 3.86 eV in the pristine composite to − 3.66 eV for COOH and − 3.71 eV for NH₂), indicating that reactivity improvements occur without significant loss of structural stability. Absolute softness (S) increases slightly upon functionalization (from − 0.82 eV⁻¹ to − 1.10 eV⁻¹ for COOH and − 1.04 eV⁻¹ for NH₂), reflecting greater flexibility in electronic response. The electrophilicity index (ω) decreases from − 1.22 eV in the pristine system to − 0.91 eV for COOH and − 0.96 eV for NH₂, suggesting a reduced electron-withdrawing tendency that can improve selectivity by favoring energetically accessible target–sensor interactions. Complementary QTAIM, MESP, NCI, and RDG analyses confirm the formation of stable non-covalent interactions and favorable electrostatic potential distributions, with alanine engaging the composite through both NH₂ and COOH binding sites. Collectively, the results identify COOH-functionalized GrO/PPy/ZnO as the most promising candidate for high-performance alanine detection, offering the optimal balance of low ionization potential, high electron affinity, enhanced softness, and maintained stability, thus establishing a robust theoretical foundation for future experimental sensor development.