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Exploring therapeutic options is crucial in the ongoing COVID-19 pandemic caused by SARS-CoV-2. Nirmatrelvir, which is a potent inhibitor that targets the SARS-CoV-2 Mpro, shows promise as an antiviral treatment. Additionally, Ivermectin, which is a broad-spectrum antiparasitic drug, has demonstrated effectiveness against the virus in laboratory settings. However, its clinical implications are still debated. Using computational methods, such as molecular docking and 100 ns molecular dynamics simulations, we investigated how Nirmatrelvir and Ivermectin interacted with SARS-CoV-2 Mpro(A). Calculations using density functional theory were instrumental in elucidating the behavior of isolated molecules, primarily by analyzing the frontier molecular orbitals. Our analysis revealed distinct binding patterns: Nirmatrelvir formed strong interactions with amino acids, like MET49, MET165, HIS41, HIS163, HIS164, PHE140, CYS145, GLU166, and ASN142, showing stable binding, with a root-mean-square deviation (RMSD) of around 2.0 Å. On the other hand, Ivermectin interacted with THR237, THR239, LEU271, LEU272, and LEU287, displaying an RMSD of 1.87 Å, indicating enduring interactions. Both ligands stabilized Mpro(A), with Ivermectin showing stability and persistent interactions despite forming fewer hydrogen bonds. These findings offer detailed insights into how Nirmatrelvir and Ivermectin bind to the SARS-CoV-2 main protease, providing valuable information for potential therapeutic strategies against COVID-19.
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Antivirales , Tratamiento Farmacológico de COVID-19 , Proteasas 3C de Coronavirus , Ivermectina , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , SARS-CoV-2 , Ivermectina/química , Ivermectina/farmacología , SARS-CoV-2/efectos de los fármacos , SARS-CoV-2/enzimología , Proteasas 3C de Coronavirus/química , Proteasas 3C de Coronavirus/antagonistas & inhibidores , Proteasas 3C de Coronavirus/metabolismo , Humanos , Antivirales/química , Antivirales/farmacología , Unión Proteica , Sulfonamidas/química , Sulfonamidas/farmacología , Sitios de Unión , Inhibidores de Proteasas/química , Inhibidores de Proteasas/farmacología , Lactamas , Leucina , Nitrilos , ProlinaRESUMEN
Recent progress in nanoelectronics suggests that stacking armchair graphene nanoribbons (AGNRs) into bilayer systems can generate materials with emergent quasiparticle properties. In this context, the impact of width changes is especially relevant. However, its effect on charged carriers remains elusive. In this work, we investigate the effect of width and interlayer interaction changes on polaron states via a hybrid Hamiltonian that couples the electronic and lattice interactions. Results show the rising of two interlayer polarons: the non-symmetric and the symmetric. The coupling strength needed to induce the transition between states depends on the nanoribbon width, being at the most extreme case of ≈174 meV. Electronic properties such as the coupling strength threshold, carrier size, and gap are shown to respect the AGNR width family 3p, 3p + 1, and 3p + 2 rule. The findings demonstrate that strong interlayer interaction simultaneously delocalizes the carriers and reduces the gap up to 0.6 eV. Additionally, it is found that some layers are more prone to share charge, indicating a potential heterogeneous stacking where a particular electronic pathway is favored. The results present an encouraging prospect for integrating AGNR bilayers in future flexible electronics.
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CONTEXT AND RESULTS: This study aimed to obtain potential energy curves within a multireference 4-component relativistic method and to present spectroscopic constants (R[Formula: see text],[Formula: see text],[Formula: see text]x[Formula: see text],[Formula: see text]y[Formula: see text], D[Formula: see text], D[Formula: see text], B[Formula: see text],[Formula: see text],[Formula: see text],[Formula: see text] ), accurate extended Rydberg analytical form, and rovibrational levels for the 6 low-lying states of the I[Formula: see text] anion. For these states, some spectroscopic constants, rovibrational levels, and an accurate analytical form are presented for the first time in literature, and they are of interest for femtosecond and dynamics experiments of I[Formula: see text] as well as for electron attachment of I[Formula: see text]. This study suggests that the inclusion of relativistic and correlation effects treated at the MRCISD+Q level is needed to obtain reliable results, specially for D[Formula: see text]. COMPUTATIONAL AND THEORETICAL TECHNIQUES: The potential energy curves of the ground and the excited states of the molecular iodine anion (I[Formula: see text]) were investigated at multireference configuration interaction (MRCISD) with Davidson size-extensivity correction (denoted as +Q) within a fully relativistic four-component relativistic framework including Breit interaction.
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CONTEXT AND RESULTS: This work aims to study the influence of the absence and presence of permanent charges on the electronic and dynamical properties of the non-covalent bound diatomic systems involving He and Li, Be as neutral and ionic partners. The charge displacement results suggest that in the formation of HeLi[Formula: see text], HeBe[Formula: see text], and HeBe[Formula: see text], the neutral He atom undergoes, in the electric field of the ion, a pronounced electronic polarization, and the natural bond order theoretical approach indicates that in the formation of the molecular orbital He acts as a weak electron donor. The energy decomposition analysis provides the dispersion and induction components as the attractive leading terms controlling the stability of all systems, confirming that the formed bond substantially maintains a non-covalent nature which is also supported by the Quantum Theory of Atoms in Molecules (QTAIM) analysis. Finally, it was found that the HeLi and HeBe neutral systems are unstable under any condition, HeLi[Formula: see text] and HeBe[Formula: see text] ionic systems are stable below 317K and 138K, respectively, while the HeBe[Formula: see text] system becomes unstable only after 3045K. COMPUTATIONAL AND THEORETICAL TECHNIQUES: The potential energy curves and interactions in all systems were studied theoretically based on coupled-cluster singles and doubles method with perturbative inclusion of triples CCSD(T) method with an aug-cc-pV5Z basis set. More precisely, it was determined the potential energy curves describing the stability of the HeLi, HeLi[Formula: see text], HeBe, HeBe[Formula: see text], and HeBe[Formula: see text] systems, the charge displacement within the formed adducts, the decomposition of their total interaction energy, the topological analysis of their bonds, their rovibrational energies, their spectroscopic constants and lifetimes.
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This work presents a study involving dimers composed of He, Ne, Ar, Kr, Xe, Rn, and Og noble gases with oganesson, a super-heavy closed-shell element (Z = 118). He-Og, Ne-Og, Ar-Og, Kr-Og, Xe-Og, Rn-Og, and Og-Og ground state electronic potential energy curves were calculated based on the 4-component (4c) Dirac-Coulomb Hamiltonian and were counterpoise corrected. For the 4c calculations, the electron correlation was taken into account using the same methodology (MP2-srLDA) and basis set quality (Dyall's acv3z and Dunning's aug-cc-PVTZ). All calculations included quantum electrodynamics effects at the Gaunt interaction level. For all the aforementioned dimers the vibration energies, spectroscopic constants (ωe, ωexe, ωeye, αe, and γe), and lifetime as a function of the temperature (which ranged from 200 to 500 K) were also calculated. The obtained results suggest that the inclusion of quantum electrodynamics effects reduces the value of the dissociation energy of all hetero-nuclear molecules with a percentage contribution ranging from 0.48% (for the He-Og dimer) to 9.63% (for the Rn-Og dimer). The lifetime calculations indicate that the Og-He dimer is close to the edge of instability and that Ng-Og dimers are relatively less stable when the Gaunt correction is considered. Exploiting scaling laws that adopt the polarizability of involved partners as scaling factors, it has also been demonstrated that in such systems the interaction is of van der Waals nature (size repulsion plus dispersion attraction) and this permitted an estimation of dissociation energy and equilibrium distance in the Og-Og dimer. This further information has been exploited to evaluate the rovibrational levels in this symmetric dimer and to cast light on the macroscopic properties of condensed phases concerning the complete noble gas family, emphasizing some anomalies of Og.
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In this work, the binding features of adducts formed by a noble gas (Ng = He, Ne, Ar, Kr, Xe, and Rn) atom and the oxygen molecule (O2) in its ground Σg-3, in the past target of several experimental studies, have been characterized under different theoretical points of view to clarify fundamental aspects of the intermolecular bond. For the most stable configuration of all Ng-O2 systems, binding energy has been calculated at the theory's CCSD(T)/aug-cc-pVTZ level and compared with the experimental findings. Rovibrational energies, spectroscopic constants, and lifetime as a function of temperature were also evaluated by adopting properly formulated potential energy curves. The nature of the interaction involved was deeply investigated using charge displacement analysis, symmetry-adapted perturbation theory (SAPT), and natural bond orbital (NBO) methods. In all adducts, it was found that the charge transfer plays a minor role, although O2 is an open shell species exhibiting a positive electron affinity. Obtained results also indicate that the dispersion attraction contribution is the main responsible for the complex stability.
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The search for new materials, with ideal electronic and magnetic properties for potential applications in nanoelectronics, has been extremely successful so far, and has paved the way for us to reimagine all technological devices. In the present work, we study the design of MgCl2 nanoribbons for applications in nanoelectronics and spintronics, by employing first-principles calculations based on density functional theory (DFT) and non-equilibrium Greens function techniques. Our results show that the properties of MgCl2 nanoribbons depend strongly not only on their geometrical form (armchair or zigzag) but also on the atoms at their edges. The armchair MgCl2 nanoribbon is a semiconductor and the zigzag nanoribbons vary from semiconducting, to metallic, to ferromagnetic, and to half-metallic, depending on the edge terminations. All these nanoribbons are very stable, with a relatively low cohesive energy per atom, and their attributes are not affected by the width of the nanoribbon. From transport calculations, we observed partial spin filtering in the ferromagnetic nanoribbon and perfect spin filtering in the two half-metallic nanoribbons. Moreover, we show how the current versus voltage curves can be fully understood by analysing the alignment of the energy levels of the electrodes. Our results corroborate the promising use of single-layer MgCl2 for the development of spintronics devices.
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In this study, all electron relativistic calculations with 4-component Dirac-Coulomb-Breit (DCB), 4-component Dirac-Coulomb (DC), Dyall's spin-free Dirac-Coulomb (SFDC), exact two-component (X2C) and Levy-Leblond non-relativistic hamiltonians calculations were performed in polyatomic closed shell E121X3 (X = F, Cl, Br) within density functional theory (DFT) with hybrid functional B3LYP, where E121 is the superheavy element (SHE) with Z = 121. The aims of this study were to investigate relativistic effects in polyatomic E121X3 (X = F, Cl, Br) and verify the importance of Gaunt effects. The results demonstrate that although the effect of Gaunt interaction is small on change equilibrium bond lengths and bonding, it is important to obtain reliable vibrational frequencies. Moreover, it is possible to use the X2C spin-free hamiltonian to lower computational costs in a fully relativistic investigation of polyatomics including the SHE of the 8th period. Finally, a comparison between electron localization function (ELF) analysis and Mulliken population analysis suggests bonding similarity between LaBr3 and E121Br3. Graphical Abstract Relativistic 4-Component calculations suggest bond similarity between LaBr3 and E121Br3.
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The present work reports the synthesis and a structural study of two novel dithiocarbazate, the 4,6-diacetylresorcinol-S-benzyldithiocarbazate (H3L1) and the 4,6-diacetylresorcinol-bis(S-benzyldithiocarbazate) (H4L2), and their Ni(II) complexes, [Ni(HL1)(Py)] (1) and [Ni2(L2)(PPh3)2] (2). Single crystal X-ray analyzes reveal mono and binuclear complexes and the metal centers with distorted square planar geometry. The analyses of the Hirshfeld surface and fingerprints plots revealed intermolecular contacts attributed to the H···H and C···H/H···C bonds. The Density Functional Theory (DFT), with the B3LYP functional and 6-311-G(d,p)/LanL2DZ basis sets, was employed to optimize the geometries of synthesized compounds. From the resulting geometries, the highest occupied and lowest unoccupied molecular orbital maps (HOMO-LUMO), orbital energy gap, electron localization function (ELF), electron density, natural bond orbital (NBO) analysis, and complexation of the ligands with Ni(II) were calculated supporting the experimental data. The ESI (+)-MS/MS data indicated the presence in solution of the characteristic fragmentation with the [H3L1]+ and [H4L2]+ molecular ions for the ligands. The pharmacological potential of the dithiocarbazate ligands and their Ni(II) complexes were evaluated in vitro against MDA-MB-231 human breast cancer cells. A remarkable cytotoxic activity was observed, more evident for free ligands than complexes at low concentrations; however, this latter showed a better dose-response pattern, being more attractive in terms of pharmacokinetics and therapeutic window.
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Complejos de Coordinación/química , Hidrazinas/química , Níquel/química , Resorcinoles/química , Línea Celular Tumoral , Supervivencia Celular/efectos de los fármacos , Complejos de Coordinación/farmacología , Cristalografía por Rayos X/métodos , Teoría Funcional de la Densidad , Humanos , Hidrazinas/farmacología , Ligandos , Estructura Molecular , Níquel/farmacología , Resorcinoles/farmacología , Espectrometría de Masas en Tándem/métodosRESUMEN
As part of our efforts to develop sustainable drugs for Alzheimer's disease (AD), we have been focusing on the inexpensive and largely available cashew nut shell liquid (CNSL) as a starting material for the identification of new acetylcholinesterase (AChE) inhibitors. Herein, we decided to investigate whether cardanol, a phenolic CNSL component, could serve as a scaffold for improved compounds with concomitant anti-amyloid and antioxidant activities. Ten new derivatives, carrying the intact phenolic function and an aminomethyl functionality, were synthesized and first tested for their inhibitory potencies towards AChE and butyrylcholinesterase (BChE). 5 and 11 were found to inhibit human BChE at a single-digit micromolar concentration. Transmission electron microscopy revealed the potential of five derivatives to modulate Aß aggregation, including 5 and 11. In HORAC assays, 5 and 11 performed similarly to standard antioxidant ferulic acid as hydroxyl scavenging agents. Furthermore, in in vitro studies in neuronal cell cultures, 5 and 11 were found to effectively inhibit reactive oxygen species production at a 10 µM concentration. They also showed a favorable initial ADME/Tox profile. Overall, these results suggest that CNSL is a promising raw material for the development of potential disease-modifying treatments for AD.
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The Lennard-Jones (LJ) and Improved Lennard-Jones (ILJ) potential models have been deeply tested on the most accurate CCSD(T)/CBS electronic energies calculated for some weakly bound prototype systems. These results are important to plan the correct application of such models to systems at increasing complexity. CCSD(T)/CBS ground state electronic energies were determined for 21 diatomic systems composed by the combination of the noble gas atoms. These potentials were employed to calculate the rovibrational spectroscopic constants, and the results show that for 20 of the 21 pairs the ILJ predictions agree more effectively with the experimental data than those of the LJ model. The CCSD(T)/CBS energies were also used to determine the ß parameter of the ILJ form, related to the softness/hardness of the interacting partners and controlling the shape of the potential well. This information supports the experimental finding that suggests the adoption of ß≈9 for most of the systems involving noble gas atoms. The He-Ne and He-Ar molecules have a lifetime of less than 1ps in the 200-500 K temperature range, indicating that they are not considered stable under thermal conditions of gaseous bulks. Furthermore, the controversy concerning the presence of a "virtual" or a "real" vibrational state in the He2 molecule is discussed.
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Accurate calculation of the acid dissociation constant (pKa) has fundamental importance for the description of molecular systems with pharmacological activities. The search for a more appropriate procedure for its determination is always welcome and has aroused increasing interest from the scientific community. In this sense, this work presents a computational study involving the combination of ten DFT functionals (M062X, M06L, B3LYP, BLYP, PBEPBE, BP86, LC-BLYP, SPBE, CAM-B3LYP, LC-PBEPBE) and HF method, eight basis set functions (6-311G, 6-311 + G, 6-311G(d,p), 6-311 + G(d,p), 6-311+ +G(d,p), 6-311(2d,2p), 6-311+ +G(2d,2p), and aug-cc-pVDZ), and three solvation models (SMD, PCM, and CPCM) for an accurate sulfachloropyridazine (SCR) pKa determination. It was found that the smallest deviation (0.02 unit of pKa) between the current study and experimental result was achieved with the BLYP/6-311 + G(d,p)/PCM combination. Therefore, this combination was extended to calculate the pKa of six SCR similar molecules selected through the eletroshape similarity method. For all these molecules, the difference between the obtained results and experimental data ranged between 0.14 and 0.69 units of pKa. This feature suggests that the obtained combination can determine pKa with experimental precision for complexes that are formed by sulfonamide functional group (SO2NHR). Graphical Abstract A computational study involving the combination of different levels of theory, basis sets and solvation models for an accurate sulfanamide pKa determination.
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In this study, the potential energy curves of the ground and the excited states of molecular fluorine anion (F[Formula: see text]) were investigated at multireference configuration interaction (MRCISD) with Davidson size-extensivity correction (denoted as +Q) within fully relativistic four-component relativistic framework including Breit interaction. Spectroscopic constants (Re, ωe, ωexe, ωeye, De,D0,Be, αe, ße, γe ), accurate extended Rydberg analytical form and rovibrational levels for ground state X:[Formula: see text] are presented, as well as spectroscopic constants for non dissociative excited states. For most states these spectroscopic constants are presented for the first time in literature and they are of interest for experimental studies, specially regarding electron attachment of F2. Results suggest that inclusion of relativistic effects at 4-component level and correlation effects treated at MRCISD+Q level are needed to obtain reliable results, which we report for X:[Formula: see text] ground state's Re, ωe and De the values of 1.999 Å, 391 cm- 1 and 1.22 eV, respectively.
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The potential energy curves (PECs) of all covalent states of Molecular Astatine (At2) have been investigated in this work within a four-component relativistic framework using the MOLFDIR program package. The ground state was determined using multireference configuration interaction with all single and double excitations including Davidson size-extensivity correction (MRCISD+Q) whereas the 22 excited states were treated by complete open shell configuration interaction (COSCI). Spectroscopic constants (Re,ωe,ωexe,ωeye, De,Be,αe,ße,Te) are presented for all states as well as vertical excitations obtained at COSCI, MRCISD and MRCISD+Q levels. In addition, it is also presented accurate extended Rydberg analytical form for the ground state X: (1)0g+.
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An integrated experimental-theoretical investigation was employed to determine rovibrational energies, spectroscopic constants, lifetime as a function of temperature in gas phase complexes of methanol with noble gas (NgHe, Ne, Ar, Kr, Xe, and Rn). Beside that, a parallel effort has been addressed to theoretically characterize the nature of intermolecular interactions determining the dissociation energy and equilibrium distance of the formed adducts. Dynamics and lifetime results reveal that, except for the CH3OH-He aggregate, all other methanol-Ng compounds are sufficiently stable under thermal conditions. Their lifetimes are larger than 1 ps for the temperature of the bulk in the range between 200 and 500 K. In addition, the current lifetime results suggest that the aggregates formed by methanol and Ng are globally more stable than corresponding complexes formed by water with Ng. From the point of view of the CCSD(T)/aug-cc-pVTZ level calculation, in all compounds, the electron densities of Ng partners are weakly polarized in the presence of CH3OH molecule. The charge-displacement curves and NBO analysis indicate that the charge transfer from Ng to methanol molecule, in general, plays a minor role, being appreciable only in the aggregate involving Ar. Finally, it was verified from the SAPT2 + (CCD)-δMP2/aug-cc-pVTZ calculations and NCI analysis that the dispersion is the essential long-range attractive contribution to the interaction energy for all studied complexes. This feature strongly suggests that these compounds are held bonded substantially by van der Waals forces. Then non-covalent intermolecular bonds are effectively formed in the gas phase, which is disturbed by small stabilizing charge-transfer contributions.
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The capability of Diffusion Quantum Monte Carlo (DMC) to produce high quality potential energy curve (PEC) was evaluated. H2+, HeH+ and LiH PECs were built by all-electron fixed-node DMC calculations. Trial wave functions were obtained from Hartree-Fock (HF) (H2+), MCSCF and CI (HeH+ and LiH) calculations multiplied by Jastrow factor. The quality of these generated PECs was analyzed throughout equilibrium distance, dissociation energy, vibrational energies and rovibrational spectroscopic constants (ωe, ωexe, ωeye, αe, γe and Be). The Discrete Variable Representation (DVR) and the Dunham approaches were used to determine the rovibrational spectroscopic constants. The PECs and the aforementioned properties were also obtained by the following methods: MCSCF/aug-cc-pV5Z (LiH), CCSD(T)/aug-cc-pV5Z (HeH+ and LiH) and HF (H2+ and HeH+) levels. The results of these DMC computations, specially the DMC-DVR procedure, are the most accurate among others DMC calculations available in the literature for these systems. They suggest that DMC can be used to achieve accurate PECs to produce spectroscopic properties with the same level of accuracy of theoretical benchmarks and experimental data of the literature.
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Previous studies have shown that the weakly bonded H2S dimer demands high level quantum chemical calculations to reproduce experimental values. We investigated the hydrogen bonding of H2S dimer using MP2 and CCSD(T) levels of theory in combination with aug-cc-pV(D,T,Q)Z basis sets. More precisely, the binding energies, potential energy curves, rovibrational spectroscopic constants, decomposition lifetime, and normal vibrational frequencies were calculated. In addition, we introduced the local mode analysis of Konkoli-Cremer to quantify the hydrogen bonding in the H2S dimer as well as providing for the first time the comprehensive decomposition of normal vibrational modes into local modes contributions, and a decomposition lifetime based on rate constant. The local mode force constant of the H2S dimer hydrogen bond is smaller than that of the water dimer, in accordance with the weaker hydrogen bonding in the H2S dimer.
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In this work, we calculate the rovibrational energies and spectroscopic constants for the systems formed by ammonia (NH3) and noble gases (Ng=He, Ne, Ar, Kr and Xe). For the spectroscopic constant calculations, we used two different methods: Dunham and another one that use rovibrational energies (here calculated by discrete variable method). In both cases, we used the improved Lennard-Jones potential energy curves (PECs). These PECs, which describe very well van der Waals systems, were built using the dissociation and equilibrium distance obtained from experiments of crossed molecular beams. The spectroscopic constant results, obtained by both methods were in excellent agreement with each other for all NH3-Ng studied systems. Also in relation to NH3-He system, we realize that although this system has a relatively small dissociation energy, it has one vibrational level. Finally, the spectroscopic constants and fundamental rovibrational energy results were used to verify the stability of each system through the lifetime decomposition.
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Benzene, toluene, ethylbenzene, and xylenes are volatile hydrocarbons known as BTEX, which present concerns about environmental problems. Density functional theory (DFT) functionals were used for the BTEX gas phase adsorption on TiO2 (110) of rutile and (101) of anatase surfaces. Dispersion terms have shown the importance to treat weak interactions and were used to study these adsorptions using plane wave DFT calculations. All BTEX molecules have the same trend for the adsorption on rutile and anatase surfaces. The inclusion of dispersion terms has a significant contribution for the interaction energy. Density of states results suggest the hybridization between the d state of pentacoordinated titanium atoms (Ti5C) and carbon p states of benzene. The adsorption energy values indicate an effective interaction between the BTEX and surfaces, mainly due to the aromatic π interaction, which is present in all adsorbates. However, for p-xylene the methyl hydrogen directs the second major influence. Graphical abstract Charge difference showing the system with the smallest interaction and the one with the largest interaction.