ABSTRACT
Due to the dramatic increase in the number of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), designing new selective and sensitive sensors for the detection of this virus is of importance. In this research, by employing full atomistic molecular dynamics (MD) simulations, the interactions of the receptor-binding domain (RBD) of the SARS-CoV-2 with phosphorene and graphene nanosheets were analyzed to investigate their sensing ability against this protein. Based on the obtained results, the RBD interactions with the surface of graphene and phosphorene nanosheets do not have important effects on the folding properties of the RBD but this protein has unique dynamical behavior against each nanostructure. In the presence of graphene and phosphorene, the RBD has lower stability because due to the strong interactions between RBD and these nanostructures. This protein spreads on the surface and has lower structural compaction, but in comparison with graphene, RBD shows greater stability on the surface of the phosphorene nanosheet. Moreover, RBD forms a more stable complex with phosphorene nanosheet in comparison with graphene due to greater electrostatic and van der Waals interactions. The calculated Gibbs binding energy for the RBD complexation process with phosphorene and graphene are -200.37 and -83.65 kcal mol-1, respectively confirming that phosphorene has higher affinity and sensitivity against this protein than graphene. Overall, the obtained results confirm that phosphorene can be a good candidate for designing new nanomaterials for selective detection of SARS-CoV-2.
ABSTRACT
Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.
Subject(s)
Biosensing Techniques , Molecular Docking Simulation , Molecular Dynamics SimulationABSTRACT
In this article, 20 ns molecular dynamic (MD) simulations and density functional theory (DFT) were used to investigate the absorption of CO2 molecules by some functionalized 1,8-diazabicyclo[5,4,0]-udec-7-ene (DBU)-based ILs. According to the MD results, the highest coordination number for NC is observed in the case of [DBUH+][Im-], which indicates that the functionalization of the imidazole anion by different alkyl groups decreases the interaction ability of the anion with CO2 molecules. The addition of water molecules to the ILs decreases the ability of the anion to interact with CO2 because of the hydrogen bond formation between the imidazole anions and water. Two different paths were proposed for CO2 absorption by the ILs, and the effect of alkyl groups on the kinetics and thermodynamics of the reaction was analyzed by using the M06-2X functional at the 6-311++G(d,p) level of theory in the gas phase and water. On the basis of the results, CO2 absorption is more favorable in [DBUH+][Im-], thermodynamically. Kinetic parameters show that the alkylation of the imidazole anion by ethyl, propyl, iso-propyl, and phenyl groups decreases the rate of CO2 absorption, because of the steric and electron-withdrawing effect of different alkyl groups. In the presence of water molecules, the lowest activation Gibbs energy is related to [DBUH+][Im-], which confirms the greater ability of this IL in CO2 absorption.
ABSTRACT
The kinetic and mechanism evaluations of the formation of cyclic carbonates by carbonyl-stabilized phosphonium ylides as an efficient and new class of organocatalysts are the main purposes of this research. Recently, it has been reported that tetraarylphosphonium salts play the role of organocatalysts in carbon dioxide conversion to cyclic carbonates. However, in this research, the oxygen atom of the carbonyl-stabilized phosphonium ylides was treated as the nucleophilic atom for the carbon dioxide activation. Two probable mechanisms were considered and analyzed by the energetic span model. The kinetic behavior of the carbonyl-stabilized phosphonium ylides in the carbon dioxide or ethylene oxide activation was justified by the molecular electrostatic potential (ESP) analysis at the nuclear position. However, it was confirmed that the activation strain model (ASM) was a more efficient tool in explaining the kinetic behaviors in the carbon dioxide or ethylene oxide activation. A change in the ESP value of the donor-acceptor interacting system (ΔΔVn) and distortion energy at the transition states (ΔEstrain(ζ)) were the outcomes of the ESP and ASM models, respectively, which showed a linear correlation. The electron localization function (ELF) concept was used to justify the kinetic behavior of the second step of the preferred mechanism, revealing that the electron-donating/withdrawing groups substituted on the organocatalysts have a remarkable effect on the electron density of the involved basin at the transition states. On the basis of different analyses, it was proposed that carbonyl-stabilized phosphonium ylides having electron-donating substituents are the best candidates for carbon dioxide conversion to cyclic carbonates.
ABSTRACT
In this work, kinetics and dynamics of the functionality of indoloquinoxaline-based dye-sensitized solar cells (DSSCs), QX22-QX25, were investigated in gas and solvent media. Quantum chemistry properties of the dyes at the excited states show that each moiety of the (D)2-A-π-A system has a specific effect on the photovoltaic properties. Solvent effect analysis shows that among ethanol, toluene, tetrahydrofuran, and methylene dichloride, toluene is the preferred medium for intra-/intermolecular charge transfer, dynamically and kinetically. Moreover, the behavior of the light harvesting efficiency (LHE) and incident photon-to-current efficiency (IPCE) are not similar, due to a strong effect of the Gibbs energy of electron injection on the energy conversion efficiency. Finally, the dye composed of -COOH as the anchoring group and thiophene as the π-spacer is the best candidate to be applied in DSSC due to its better efficiency originated from a lower electrophilicity and electronic chemical potential.
ABSTRACT
Carbon materials have been regarded as promising agents for hydrogen storage because of properties such as their light weight, acceptable affinity of carbon for hydrogen and high specific surface area. We can identify many different carbon materials which have been studied extensively such as activated carbons (AC) graphene sheets (GS), carbon nanotubes (CNTs) and other derivative carbon materials derived from theoretical and experimental methods such as g-C3N4, graphyne and carbon nanolayer. These materials can be modified by additional ingredients like free metals, metal oxides, and alloys to improve their hydrogen storage capacity. In this short review article, we attempt to introduce new, reliable, complete and categorised data for researchers concentrating on articles from the last five years (2013-2017) relating to hydrogen storage.
ABSTRACT
The catalytic cycle of a new derivative of ebselen, 1, was elucidated via three steps by the density functional theory and solvent-assisted proton exchange procedure involving indirect proton exchange through a hydrogen-bonded transfer network. Different behaviors of the aromatic and aliphatic thiols were investigated in the reduction of selenoxide (step 2 â 3) and selenurane (step 3 â 1) based on their nucleophilicity. The reduction of selenoxide in the presence of thiophenol (ΔG = 15.9 kcal·mol-1) is faster than that of methanethiol (ΔG = 29.3 kcal·mol-1), and methanethiol makes the reduction of selenoxide unspontaneous and kinetically unfavorable (ΔG = 2.8 kcal·mol-1). The nucleophilic attack may be enhanced by using the thiophenol backbone at the selenium center to lower the energy barrier of the selenoxide reduction (ΔG = 15.9 kcal·mol-1). On the basis of the turnover frequency calculations, during the catalytic cycle, the rate of the reaction was analyzed and discussed. Low values of the electron density and Laplacian at the transition states are the evidence of the covalent O-H and O-O bonds rupture in the presence of methanethiol and thiophenol. The nature of the critical bond points was characterized, using the quantum theory of atoms in molecules, based on the electron location function and localized orbital locator values. Finally, the charge transfer process at the rate-determining step was investigated based on the natural bond orbital analysis.
Subject(s)
Biocatalysis , Biomimetic Materials/chemistry , Glutathione Peroxidase/chemistry , Glutathione Peroxidase/metabolism , Models, Chemical , Nanostructures/chemistry , Sulfhydryl Compounds/chemistry , Biomimetics , Kinetics , Quantum Theory , Sulfhydryl Compounds/metabolism , ThermodynamicsABSTRACT
The kinetics and mechanism of CO2 absorption by ionic liquids (ILs) were studied, theoretically. The studied ILs are composed of 1-ethyl-3-methylimidazolium [Emim]+ as the cation with a general formula of the [Emim][X] (X = Gly-, Ala-, Lys-, Arg-). To investigate the alkyl chain length and the number of the amine group effects on the CO2 absorption, different amino acid anions were chosen. On the basis of the enthalpy changes during CO2 capture, a chemisorption nature is confirmed. An increase in the number of amine (-NH2) groups in the ILs structures, facilitates the CO2 absorption. According to kinetic results, the rate of CO2 absorption by [Emim][Gly] is higher than that of [Emim][Ala]. This can be interpreted by a higher steric hindrance in [Emim][Ala] due to an additional methyl group in the amino acid chain. Donor-acceptor interactions and C-N bond formation were investigated by natural bond orbital analysis. Moreover, topological studies show a covalent nature for the C-N bond critical point that showing CO2 capture is a chemisorption process. Finally, on the basis of kinetic energy results, donor-acceptor interaction and topological analysis, [Emim][Arg] is proposed as the best candidate for CO2 absorption from the kinetic and thermodynamic viewpoints.
ABSTRACT
Hydrogen sulfide (H2S) and carbon dioxide (CO2) adsorption on a series of the aliphatic amino acid ionic liquids (AAILs) composed of N7,N9- dimethyladeninium cation with amino acid anions (AA = Gly, Ala, Val, Leu, and Ile) as the functionalized ILs with dual groups of amine have been investigated. On the basis of the obtained data, the possible sites of H2S adsorption are twice those of CO2 on the ionic liquids, and also the average adsorption energy of H2S (ΔE = -51.5 kJ mol-1) in the most stable region of adsorption is twice greater than that of CO2 (ΔE = -25.5 kJ mol-1). An increase in the length of the side chain of the amino acids increases the interaction energy of the H2S and CO2 capture (on the amine group of the [AA]- anions). Quantum theory of atoms in molecules analysis confirmed the noncovalent nature of the N···C bond formed between CO2 and N atom in both of the amine groups and S-H···O and S-H···N bond critical points of H2S on [dMA][AA]. Natural bond orbital analysis indicates that charge transfer in H2S adsorption is more important than CO2 capture. Finally, a correlation between the adsorption energy and the sum of stability energies (∑E(2)) in the most stable region has been obtained and discussed.
ABSTRACT
Theoretical studies, including quantum chemistry (QM) calculations and 25 ns molecular dynamic (MD) simulations, were performed on two types of hybrid cyclic nanopeptides (HCNPs) that are constructed of tren-capped cryptand (HCNP1) and 1,3,5-triethylbenzene-capped cryptand (HCNP2) for selective complex formation with OAC-, NO3-, HSO4-, F-, Br-, and Cl- ions in the gas phase and DMSO. Obtained data by M05-2X, M05-2X-D3, B3LYP, and B3LYP-D3 functionals indicated that HCNPs form a stable complex with F- in comparison to other ions. DFT-D3 results and quantum theory of atoms in molecules (QTAIM) analysis indicated that dispersion and electrostatic interactions are the most important driving forces in HCNP-ion complex formation, respectively. Moreover, HOMO-LUMO analysis reveals that the reactivity of HCNP2, due to a lower band gap, is more than HCNP1. High sensing ability of the studied HCNPs for different ions was confirmed by Fermi level shifting of HNCPs to higher values during the complex formation. Finally, MD simulation results in DMSO are in good agreement with QM calculations and indicate that F- forms the most stable complexes with HCNPs because of stronger electrostatic interactions.
ABSTRACT
Density functional theory and solvent-assisted proton exchange methods have been applied for computational modeling of the catalytic cycle of selenol zwitterion anion from the kinetic and thermodynamic viewpoints. Selenol zwitterion anion has been represented as an effective glutathione peroxidase nanomimic. It reduces peroxides through a three-step pathway. In the first step, seleninic acid is produced through deprotonating of the selenol zwitterion anion in the presence of the hydrogen peroxide. Seleninic acid reacts with a thiol to form selenylsulfide in the second step. In the last step, selenylsulfide is reduced by the second thiol and regenerates selenolate anion through disulfide formation. Selenol zwitterion anion in comparison to more widely studied compounds such as ebselen has a good activity to react with hydrogen peroxide and producing seleninic acid. The energy barrier of this reaction is 11.7kcalmol-1 which is smaller than the reported enzyme mimics. Moreover, the reactions of seleninic acid and selenylsulfide with methanethiol, which is used as a nucleophile, are exothermic by -18.4 or -57.0kcalmol-1, respectively. Based on the global electron density transfer value of -0.507 e from the natural atomic charge analysis, an electronic charge depletion at the transition state (TS), electron-donor substitutions on the selenolate facilitates the reduction reaction, effectively. Finally, the nature of the bond formation/cleavage at the TS has been quantitatively described by using the topological analyses.
Subject(s)
Computer Simulation , Glutathione Peroxidase/chemistry , Models, Chemical , Selenium Compounds/chemistry , Catalysis , KineticsABSTRACT
To elucidate the role of a derivative of ebselen as a mimic of the antioxidant selenoenzyme glutathione peroxidase, density functional theory and solvent-assisted proton exchange (SAPE) were applied to model the reaction mechanism in a catalytic cycle. This mimic plays the role of glutathione peroxidase through a four-step catalytic cycle. The first step is described as the oxidation of 1 in the presence of hydrogen peroxide, while selenoxide is reduced by methanthiol at the second step. In the third step of the reaction, the reduction of selenenylsulfide occurs by methanthiol, and the selenenic acid is dehydrated at the final step. Based on the kinetic parameters, step 4 is the rate-determining step (RDS) of the reaction. The bond strength of the atoms involved in the RDS is discussed with the quantum theory of atoms in molecules (QTAIM). Low value of electron density, ρ(r), and positive Laplacian values are the evidence for the covalent nature of the hydrogen bonds rupture (O30-H31, O33-H34). A change in the sign of the Laplacian, L(r), from the positive value in the reactant to a negative character at the transition state indicates the depletion of the charge density, confirming the N5-H10 and O11-Se1 bond breaking. The analysis of electron location function (ELF) and localized orbital locator (LOL) of the Se1-N5 and Se1-O11 bonds have been done by multi-WFN program. High values of ELF and LOL at the transition state regions between the Se, N, and O atoms display the bond formation. Finally, the main donor-acceptor interaction energies were analyzed using the natural bond orbital analysis for investigation of their stabilization effects on the critical bonds at the RDS.
Subject(s)
Azoles/chemistry , Glutathione Peroxidase/chemistry , Nanostructures/chemistry , Organoselenium Compounds/chemistry , Quantum Theory , Azoles/metabolism , Biocatalysis , Glutathione Peroxidase/metabolism , Isoindoles , Models, Molecular , Molecular Structure , Organoselenium Compounds/metabolismABSTRACT
In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.
Subject(s)
Lipopeptides/chemistry , Molecular Dynamics Simulation , Nanotubes/chemistry , Peptides, Cyclic/chemistry , Quantum Theory , Lipid Bilayers/chemistry , ThermodynamicsABSTRACT
Molecular dynamic simulations were performed to investigate the stability of heterocyclic peptide nanotubes composed of 1,4-disubstituted-1,2,3-triazol ε-amino acid. 45 ns MD simulations were conducted on the cyclic peptide nanotube (CPNT) and cyclic peptide dimer in methanol, chloroform, and water and revealed that these structures are more stable in nonpolar solvents. MM-PBSA and MM-GBSA calculations were employed to analyze the solvent effect on the stability and length of the CPNT. These calculations showed that CPNT in chloroform was more stable and longer as compared to other solvents. In addition, the effect of the guest molecule (ethanol) inside the dimer and CPNT was investigated. The obtained results confirmed that guest molecule(s) stabilized the dimer and CPNT in all solvents. Quantum chemistry calculations on the cyclic peptide dimer were performed at the M06-2X/6-31G(d) level in the gas phase and three solvents. The obtained results from the quantum chemistry study were in good agreement with the MD simulation results. DFT calculations showed that the guest molecule stabilized the dimer structure and electrostatically interacted with the cyclic peptide dimer. Finally, for investigation of the solvent effects on the hydrogen bonds of the cyclic peptide dimer, NBO and AIM analysis were performed.
Subject(s)
Molecular Dynamics Simulation , Nanotubes/chemistry , Peptides, Cyclic/chemistry , Quantum Theory , Solvents/chemistry , Molecular ConformationABSTRACT
Quantitative structure activity relationship (QSAR) for the anticancer activity of Fe(III)-salen and salen-like complexes was studied. The methods of density function theory (B3LYP/LANL2DZ) were used to optimize the structures. A pool of descriptors was calculated: 1497 theoretical descriptors and quantum-chemical parameters, shielding NMR, and electronic descriptors. The study of structure and activity relationship was performed with multiple linear regression (MLR) and artificial neural network (ANN). In nonlinear method, the adaptive neuro-fuzzy inference system (ANFIS) was applied in order to choose the most effective descriptors. The ANN-ANFIS model with high statistical significance (R (2) train = 0.99, RMSE = 0.138, and Q (2) LOO = 0.82) has better capability to predict the anticancer activity of the new compounds series of this family. Based on this study, anticancer activity of this compound is mainly dependent on the geometrical parameters, position, and the nature of the substituent of salen ligand.
Subject(s)
Antineoplastic Agents/chemistry , Ferric Compounds/chemistry , Antineoplastic Agents/pharmacology , Cell Survival/drug effects , Ferric Compounds/pharmacology , Humans , Linear Models , MCF-7 Cells , Neural Networks, Computer , Quantitative Structure-Activity RelationshipABSTRACT
A theoretical density functional theory (DFT) study was employed to investigate solvent effects on a retro-cheletropic ene reaction. The use of a nonpolar solvent in this retro-ene reaction is desirable to improve the reaction rate. Interactions between 14 different solvents and the reaction mixtures (reactant and transition state) were considered using DFT solvation calculations. These results were used to determine the role of solvents on the rate constants. Theoretical calculations at the B3LYP/6-311++G(d,p) level revealed that in the presence of solvents with low polarity the reaction becomes faster, which is in accordance with experimental data. Transition state-solvent interactions were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations between electron densities in bond critical points of the C-S bond and interaction energy as well as vibrational frequencies at the transition state have been investigated.
ABSTRACT
Understanding the effective factors in the performance of some Oligo (p-phenylenes) (OPPs) and Polycyclic Aromatic Hydrocarbons (PAHs), as efficient organocatalysts in photocatalytic CO2 transformations are the main goals of this investigation. The studies are based on density functional theory (DFT) calculations on the mechanistic aspects of C-C bond formation through a coupling reaction between CO2â¢- and amine radical. The reaction is performed through two successive single electron transfer steps. After careful kinetic investigations by Marcus' theory rules, powerful descriptors are used to describe the behavior of observed barrier energies of electron transfer steps. The studied PAHs and OPPs consist of different numbers of rings. Thus, it can be considered different charge densities, afforded from π electrons, of PAHs and OPPs that cause distinguished efficiency in kinetic aspects of electron transfer steps. Electrostatic Surface Potential (ESP) analyses reveal a good relationship between the charge density of the studied organocatalysts in single electron transfer (SET) steps and the kinetic parameters of the steps. Moreover, the contribution of rings in the framework of PAHs and OPPs would be another effective factor in the barrier energies of SET steps. Aromatic properties of the rings, studied by the Anisotropy of the Current-Induced Density (ACID), Nucleus-Independent Chemical Shift (NICS), the multi-center bond order (MCBO), and AV1245 Indexes, are the other impressive factors in the role of rings in SET steps. The results show that the aromatic properties of the rings are not similar to each other. Higher aromaticity affords remarkable reluctance of the corresponding ring to participate in SET steps.
Subject(s)
Electrons , Polycyclic Aromatic Hydrocarbons , Carbon Dioxide , Amino Acids , Polycyclic Aromatic Hydrocarbons/chemistry , AminesABSTRACT
Cadmium (Cd) as a toxic element that is widely present in water, soil, and air has important effects on human health, therefore proposing an accurate and selective method for detection of this element is of importance. In this article, by employing full atomistic molecular dynamics (MD) simulations and density functional theory dispersion corrected (DFT-D3) calculations, the effects of 6-mercaptonicotinic acid (MNA) and L-cysteine (CYS) on the stability of gold nanoparticles (AuNPs) and their sensitivity against Cd2+ were investigated. The obtained results indicate that pure AuNPs are not stable in water, while functionalized AuNPs with CYS and MNA groups have considerable stability without aggregation. In other words, the functional groups on the surface of AuNPs elevate their resistance against aggregation by an increase in the repulsive interactions between the gold nanoparticles. Moreover, functionalized AuNPs have considerable ability for selective detection of Cd2+ in the presence of different metal ions. Based on the MD simulation results, MNA-CYS-AuNPs (functionalized AuNPs with both functional groups) have the maximum sensitivity against Cd2+ in comparison with MNA-AuNPs and CYS-AuNPs due to the strong electrostatic interactions. DFT-D3 calculations reveal that the most probable interactions between the metal ions and functional groups are electrostatic, and Cd2+ can aggregate functionalized AuNPs due to strong electrostatic interactions with MNA and CYS groups. Moreover, charge transfer and donor-acceptor analyses show that molecular orbital interactions between the functional groups and Cd2+ can be considered as the driving force for AuNPs aggregation. A good agreement between the theoretical results and experimental data confirms the importance of the molecular modeling methods as a fast scientific protocol for designing new functionalized nanoparticles for application in different fields.
Subject(s)
Cadmium/analysis , Gold/chemistry , Metal Nanoparticles/chemistry , Nanotechnology/methods , Nicotinic Acids/chemistry , Water Pollutants, Chemical/analysis , Barium/chemistry , Colorimetry , Cysteine/chemistry , Ions , Limit of Detection , Models, Molecular , Molecular Dynamics Simulation , Niacin/chemistry , Quantum Theory , Solvents , Static Electricity , Thermodynamics , WaterABSTRACT
In this research, through the use of molecular dynamics (MD) simulations, the ability of gold nanoparticles (AuNPs) functionalized by different groups, such as 3-mercaptoethylsulfonate (Mes), undecanesulfonic acid (Mus), octanethiol (Ot), and a new peptide, to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated. According to the crystal structure of angiotensin-converting enzyme 2 (ACE2), which binds to the SARS-CoV-2 receptor binding domain (RBD), 15 amino acids of ACE2 have considerable interaction with RBD. Therefore, a new peptide based on these amino acids was designed as the functional group for AuNP. On the basis of the obtained results, functionalized AuNPs have remarkable effects on the RBD and strongly interact with this protein of SARS-CoV-2. Among the studied nanoparticles, the AuNP functionalized by new peptide forms a more stable complex with RBD in comparison with ACE2, which is the human receptor for SARS-CoV-2. Different analyses confirm that the designed AuNPs can be good candidates for antiviral agents against COVID-19 disease.
Subject(s)
Angiotensin-Converting Enzyme 2/chemistry , Antiviral Agents/chemistry , Gold/chemistry , Metal Nanoparticles/chemistry , Models, Theoretical , Receptors, Coronavirus/chemistry , SARS-CoV-2/drug effects , Antiviral Agents/pharmacology , Binding Sites , Drug Design , Gold/pharmacology , Humans , Molecular Dynamics Simulation , Peptides/chemistry , Protein Binding , COVID-19 Drug TreatmentABSTRACT
In this work, systematic density functional theory (DFT) calculations were performed to study the interactions of various metal ions (Al3+, Fe3+, Co2+, Ni2+, Cu2+, and Zn2+) and the clinically useful chelating agent called deferiprone (DFP) at the M05-2X/6-31G(d) level of theory. The thermodynamic parameters of metal-deferiprone complexes were determined in water. Based on the obtained data, the theoretical binding energy trend is as follows: Al3+ > Fe3+ > Cu2+ > Ni2+ > Co2+ > Zn2+, confirming that [Al(DFP)3] has the most interaction energy. Moreover, Natural bond orbital analysis was employed to determine and analyze the natural charges on different atoms and charge transfer between the metal ions and ligands (oxygen atoms) as well as the interaction energy (E(2)) values. The calculated value of Æ©E(2) (donor-acceptor interaction energy) for [Al(DFP)3] complex is higher than other complexes, which is according to energy analysis. To confirm the type of effective interactions and bonding properties in the water, the quantum theory of atoms in molecules (QTAIM) analysis was applied. QTAIM analysis confirmed that the strongest M - O bond is found in the [Al(DFP)3] complex. The calculated topological properties at the bond critical points, such as the ratio of the kinetic energy density to the potential energy density, -G(r)/V(r), electronic energy density, H(r), confirm that M - O bonds in the Al-deferiprone complex are non-covalent, while in other complexes, they are electrostatic and partially covalent.