Computational nanochemistry report on the oxicams--conceptual DFT indices and chemical reactivity

Understanding the Enzyme (S)-Norcoclaurine Synthase Promiscuity to Aldehydes and Ketones

The (S)-norcoclaurine synthase from Thalictrum flavum (TfNCS) stereoselectively catalyzes the Pictet-Spengler reaction between dopamine and 4-hydroxyphenylacetaldehyde to give (S)-norcoclaurine. TfNCS can catalyze the Pictet-Spengler reaction with various aldehydes and ketones, leading to diverse tetrahydroisoquinolines. This substrate promiscuity positions TfNCS as a highly promising enzyme for synthesizing fine chemicals. Understanding carbonyl-containing substrates' structural and electronic signatures that influence TfNCS activity can help expand its applications in the synthesis of different compounds and aid in protein optimization strategies. In this study, we investigated the influence of the molecular properties of aldehydes and ketones on their reactivity in the TfNCS-catalyzed Pictet-Spengler reaction. Initially, we compiled a library of reactive and unreactive compounds from previous publications. We also performed enzymatic assays using nuclear magnetic resonance to identify some reactive and unreactive carbonyl compounds, which were then included in the library. Subsequently, we employed QSAR and DFT calculations to establish correlations between substrate-candidate structures and reactivity. Our findings highlight correlations of structural and stereoelectronic features, including the electrophilicity of the carbonyl group, to the reactivity of aldehydes and ketones toward the TfNCS-catalyzed Pictet-Spengler reaction. Interestingly, experimental data of seven compounds out of fifty-three did not correlate with the electrophilicity of the carbonyl group. For these seven compounds, we identified unfavorable interactions between them and the TfNCS. Our results demonstrate the applications of in silico techniques in understanding enzyme promiscuity and specificity, with a particular emphasis on machine learning methodologies, DFT electronic structure calculations, and molecular dynamic (MD) simulations.

Vital role of CYP450 in the biodegradation of antidiabetic drugs in the aerobic activated sludge system and the mechanisms

The extensive use of antidiabetic drugs (ADDs) and their detection in high concentrations in the environment have been extensively documented. However, the mechanism of ADDs dissipation in aquatic environments is still not well understood. This study thoroughly investigates the dissipation behavior of ADDs and the underlying mechanisms in the aerobic activated sludge system. The results indicate that the removal efficiencies of ADDs range from 3.98% to 100% within 48 h, largely due to the biodegradation process. Additionally, the gene expression of cytochrome P450 (CYP450) is shown to be significantly upregulated in most ADDs-polluted samples (P < 0.05), indicating the vital role of CYP450 enzymes in the biodegradation of ADDs. Enzyme inhibition experiments validated this hypothesis. Moreover, molecular docking and simulation results indicate that a strong correlation between the biodegradation of ADDs and the interactions between ADDs and CYP450 (Ebinding). The differences in dissipation behavior among the tested ADDs are possibly due to their electrophilic characteristics. Overall, this study makes the initial contribution to a more profound comprehension of the crucial function of CYP450 enzymes in the dissipation behavior of ADDs in a typical aquatic environment.

The Pseudo Jahn-Teller effect and NBO analysis for untangling the symmetry breaking in the planar configurations of M2X4+ (M = Si, Ge and X = Cl, Br, I): effect on electronic structure and chemical properties

CONTEXT

The Pseudo Jahn- Teller effect is a significant tool for evaluating molecular distortion and symmetry breaking. The PJT effect associated with NBO analysis can be a powerful method for studying the structural properties variations arising from D2h → C2h distortions. The theoretical studies on Si2X4+ and Ge2X4+ radical cations have been rare. The calculations have shown that C2h non-planar structures are more stable than planar structures with D2h symmetry. The [Formula: see text] PJTE problem of M2X4+ compounds is a result of the coupling between the ground B3u state and the exited B1u state in the Qb2g direction causes. Also, the difference in M and X atoms can affect the PJT instability of compounds. The findings of this work show that the energy gap between the ground and excited states that have D2h symmetry decreases from M2Cl4+ to M2I4+ and increases from Si2X4+ to Ge2X4+. In fact, there is a significant relationship between instability of high-symmetry configurations, geometric parameters, electron delocalization, chemical hardness, electronegativity, electrophilicity index, and PJT stabilization energies. These results may serve to evaluate the distortion of similar systems.

METHODS

The structures of Si2X4+ and Ge2X4+ are optimized by LC-BLYP, M06-2X, and B3LYP methods with def2-TZVPP basis set in GAMESS software. The details of the excited states of compounds are studied by the TD-DFT method. NBO analysis for planar and non-planar structures is carried out at B3LYP/def2-TZVPP level by the NBO 5. G program that demonstrates HOMO, LUMO, ED, bonding and antibonding orbital occupancies, bond order, and E2.

Performance and degradation pathway of florfenicol antibiotic by nitrogen-doped biochar supported zero-valent iron and zero-valent copper: A combined experimental and DFT study

Fluorinated compounds are a class of organic substances resistant to degradation. Although zero-valent iron (Fe0) has a promising reducing capability, it still fails to degrade fluorine-containing antibiotics (i.e., florfenicol) efficiently. In this study, we applied a simple one-pot pyrolytic approach to synthesize nitrogen-doped biochar supported Fe0 and zero-valent copper (Cu0) composite (Fe/Cu@NBC) and investigated its performance on florfenicol removal. The results clearly showed that approximately 91.4% of florfenicol in the deionized water was removed by Fe/Cu@NBC within 8 h. As the reaction time was extended to 15 d, the total degradation rate of florfenicol reached 96.6%, in which the defluorination and dechlorination rates were 73.2% and 82.1%, respectively. Both experimental results and density functional theory calculation suggested that ∙OH and ·O2- triggered β-fluorine elimination, resulting in defluorination prior to dechlorination. This new finding was distinct from previous viewpoints that defluorination was more difficult to occur than dechlorination. Fe/Cu@NBC also had a favorable performance for removal of florfenicol in surface water. This study provides a new insight into the degradation mechanism and pathway of florfenicol removal in the Fe/Cu@NBC system, which can be a promising alternative for remediation of fluorinated organic compounds in the environment.

Spectral, NBO, NLO, NCI, aromaticity and charge transfer analyses of anthracene-9,10-dicarboxaldehyde by DFT

Anthracene-9,10-dicarboxaldehyde (ADCA) is a polynuclear aromatic compound that has a planar structure with double bonds which are in conjugation. The molecule is subjected to theoretical investigation with DFT/B3LYP/6-311++G(d,p) basis set to find out the electronic structural properties and stability. Theoretical and experimental vibrational analyses are carried out. NBO studies predict that the molecule has high stability. NCI interaction studies reveal that Van der Waals force and steric effect are seen in the molecule. A shaded surface map with a projection of LOL analysis pointed out that electron depletion area is seen in this molecule. The tunnelling current is more in the boundary rings than the central ring. It is docked with the protein 4COF and the binding energy is found to be -6.6 kcal/mol. Electrons excitation analysis is performed and found that local excitation takes place for the lowest five excitations. The aromaticity of the molecule is also thoroughly investigated.

Multiplicity spin, structure, and charge of iron-verdohemeoxygenase complex: A comparison study by the DFT method

Recently the three-dimensional structure of verdoheme heme oxygenase complex was revealed. However, many parameters of verdoheme heme oxygenase’s complex structure and their role and function on Heme degradation were unknown. In this work the structure of iron verdoheme in complex with heme oxygenase was compared by the density functional theory (DFT)-based B3LYP method using the 6-31G basis set. Many parameters such as charge of verdoheme and iron as central metal, electron distribution, spin multiplicity of the molecule and proximal substituents effects on verdoheme ring stabilization and their arrangement are discussed and compared for twelve different conformations of the molecules to find the most energetically stable states.

Density functional theory, molecular docking and bioassay studies on (S)-2-hydroxy-N-(2S,3S,4R,E)-1,3,4 trihydroxyicos-16-en-2-yl)tricosanamide

A novel indigoferamide-A, earlier isolated from the seeds of Indigofera heterantha Wall was characterized using density functional theory, molecular docking and bioassays studies. Density functional theory calculations were performed at B3LYP/6-31G(d,p) to gain geometric insight of the compound. Conformational analyses have been performed around three important dihedral angles to explore the lowest energy structure and conformer. The simulated vibrational spectrum of the compound at B3LYP/6-31G(d,p) was scaled with two scaling factors, and the scaled harmonic vibrations shows nice correlation with the experimental values. 1H and 13C NMR chemical shifts were calculated using Cramer's re-parameterized function W04 at 6- 31G(d,p) basis set. Several conformers lying within 2 kcal mol-1 of the minimum energy conformer were considered; however, the chemical shifts were not significantly different among these conformers. The Gaussian averaged theoretical 1H and 13C chemical shifts correlate nicely with the experimental data. Electronic properties such as band gap, ionization potential and electron affinities were also simulated for the first time, however, no comparison could be made with the experiment. The compound was also screened for urease, antiglycation activities and the theoretical explanation of the results is provided based on molecular docking simulations.

Blue M2: an intermediate melanoidin studied via conceptual DFT

In this computational study, ten density functionals, viz. CAM-B3LYP, LC-ω PBE, M11, M11L, MN12L, MN12SX, N12, N12SX, ω B97X, and ω B97XD, related to the Def2TZVP basis sets, are assessed together with the SMD solvation model for calculation of the molecular properties and structure of blue-M2 intermediate melanoidin pigment. All the chemical reactivity descriptors for the system are calculated via conceptual density functional theory (DFT). The active sites suitable for nucleophilic, electrophilic, and radical attacks are selected by linking them with the Fukui function indices, electrophilic Parr functions, and condensed dual descriptors Δf(r), respectively. The prediction of the maximum absorption wavelength is considerably accurate relative to its experimental value. The study reveals that the MN12SX and N12SX density functionals are the most appropriate density functionals for predicting the chemical reactivity of the molecule under study.

Conceptual DFT Study of the Local Chemical Reactivity of the Colored BISARG Melanoidin and Its Protonated Derivative

This computational study assessed eight fixed RSH (range-separated hybrid) density functionals that include CAM-B3LYP, LC-ωPBE, M11, MN12SX, N12SX, ωB97, ωB97X, and ωB97XD related to the Def2TZVP basis sets together with the SMD solvation model in the calculation the molecular structure and reactivity properties of the BISARG intermediate melanoidin pigment (5-(2-(E)-(Z)-5-[(2-furyl)methylidene]-3-(4-acetylamino-4-carboxybutyl)-2-imino-1,3-dihydroimidazol-4-ylideneamino(E)-4-[(2-furyl)methylidene]-5-oxo-1H-imidazol-1-yl)-2-acetylaminovaleric acid) and its protonated derivative, BISARG(p). The chemical reactivity descriptors for the systems were calculated via the Conceptual Density Functional Theory. The choice of active sites applicable to nucleophilic, electrophilic as well as radical attacks were made by linking them with Fukui functions indices, electrophilic and nucleophilic Parr functions, and the condensed Dual Descriptor Δf(r). The study found the MN12SX and N12SX density functionals to be the most appropriate in predicting the chemical reactivity of the molecular systems under study starting from the knowledge of the HOMO, LUMO, and HOMO-LUMO gap energies.

Molecular Reactivity and Absorption Properties of Melanoidin Blue-G1 through Conceptual DFT

This computational study presents the assessment of eleven density functionals that include CAM-B3LYP, LC-wPBE, M11, M11L, MN12L, MN12SX, N12, N12SX, wB97, wB97X and wB97XD related to the Def2TZVP basis sets together with the Solvation Model Density (SMD) solvation model in calculating the molecular properties and structure of the Blue-G1 intermediate melanoidin pigment. The chemical reactivity descriptors for the system are calculated via the conceptual Density Functional Theory (DFT). The choice of the active sites related to the nucleophilic, electrophilic, as well as radical attacks is made by linking them with the Fukui function indices, the electrophilic Parr functions and the condensed dual descriptor Δ f ( r ) . The prediction of the maximum absorption wavelength tends to be considerably accurate relative to its experimental value. The study found the MN12SX and N12SX density functionals to be the most appropriate density functionals in predicting the chemical reactivity of the studied molecule.

Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals

Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly.

Computational Prediction of the Protonation Sites of Ac-Lys-(Ala)n-Lys-NH2 Peptides through Conceptual DFT Descriptors

Six density functionals (M11, M11L, MN12L, MN12SX, N12, and N12SX) in connection with the Def2TZVP basis set and the SMD solvation model (water as a solvent) have been assessed for the calculation of the molecular structure and properties of several peptides with the general formula Ac-Lys-(Ala)n-Lys-NH2, with n = 0 to 5. The chemical reactivity descriptors for these systems have been calculated through Conceptual density functional theory (DFT). The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices, the condensed dual descriptor Δf(r), and the electrophilic Parr functions. The results allowed the prediction of the protonation sites of the peptides and rendered a qualitative explanation of the difference in pKa of the two Lys groups.

Application of DFT concepts to the study of the chemical reactivity of some resveratrol derivatives through the assessment of the validity of the “Koopmans in DFT” (KID) procedure

The validity of the “Koopmans in DFT” (KID) procedure have been assessed by means of the calculation of several Conceptual DFT reactivity descriptors calculated through a [Formula: see text]SCF procedure compared with the results of the HOMO and LUMO energies of the neutral system. Three resveratrol derivatives were considered: cis- and trans-piceid and resveratrone-6-O-[Formula: see text] glucoside. The Minnesota latest family of density functionals have been considered for the calculations in connection with water as a solvent simulated with the SMD parametrization. It is shown that the range-separated hybrids MN12SX and N12SX fulfill the KID procedure with great accuracy.

Chemical Reactivity Theory Study of Advanced Glycation Endproduct Inhibitors

Several compounds with the known ability to perform as inhibitors of advanced glycation endproducts (AGE) have been studied with Density Functional Theory (DFT) through the use of a number of density functionals whose accuracy has been tested across a broad spectrum of databases in Chemistry and Physics. The chemical reactivity descriptors for these systems have been calculated through Conceptual DFT in an attempt to relate their intrinsic chemical reactivity with the ability to inhibit the action of glycating carbonyl compounds on amino acids and proteins. This knowledge could be useful in the design and development of new drugs which can be potential medicines for diabetes and Alzheimer’s disease.

A conceptual DFT study of the molecular properties of glycating carbonyl compounds

Several glycating carbonyl compounds have been studied by resorting to the latest Minnesota family of density functional with the objective of determinating their molecular properties. In particular, the chemical reactivity descriptors that arise from conceptual density functional theory and chemical reactivity theory have been calculated through a [Formula: see text]SCF protocol. The validity of the KID (Koopmans' in DFT) procedure has been checked by comparing the reactivity descriptors obtained from the values of the HOMO and LUMO with those calculated through vertical energy values. The reactivity sites have been determined by means of the calculation of the Fukui function indices, the condensed dual descriptor [Formula: see text] and the electrophilic and nucleophilic Parr functions. The glycating power of the studied compounds have been compared with the same property for simple carbohydrates.Graphical abstractSeveral glycating carbonyl compounds have been studied by resorting to the latest Minnesota family of density functional with the objective of determinating their molecular properties, the chemical reactivity descriptors and the validity of the KID (Koopmans' in DFT) procedure.

Spectroscopic and density functional theory studies of 7-hydroxy-3'-methoxyisoflavone: A new isoflavone from the seeds of Indigofera heterantha (Wall)

A new isoflavone 7-hydroxy 3'-methoxyisoflavone (1) is isolated from the seeds of Indigofera heterantha. The structure of this new compound was established using spectroscopic techniques such as ID, 2D NMR, and mass spectrometry. Density functional theory calculations are carried out for the first time for geometric, electronic and spectroscopic properties of 1 (isoflavone). DFT calculations have been performed at B3LYP/6-311G(d,p) level of theory for obtaining geometric and spectroscopic properties of compound 1. The simulated vibrational spectrum of compound 1 at B3LYP/6-311G(d,p) shows nice correlation with the experimental IR spectrum after a scaling factor of 0.973. (1)H and (13)C NMR chemical shifts were calculated using Cramer's re-parameterized function WP04 at 6-311G(d,p) basis set, and show nice correlation with the experimental data. Four conformers were considered for NMR chemical shift calculations. Electronic properties such as band gap, Ionization potential and electron affinities were also simulated for the first time; however, no comparison could be made with the experiment.

Impact of Lewis base on chemical reactivity and separation efficiency for hydrated fourth-row transition metal (II) complexes: an ONIOM DFT/MM study

In this paper, two-layer ONIOM combinations of high-level quantum mechanics (QM) and inexpensive molecular mechanics (MM) are successfully used to investigate the structural characters of metal (M, all the transition metals in the fourth period)-H2O-Lewis base (A(-)) complexes. Global and local descriptors of chemical reactivity and selectivity from conceptual density functional theory are employed to show the properties of the active complexes of M(H2O)2A2 and to study the effect of the Lewis base for the separation of transition metal ions. It is shown that chemical potential, hardness, electrophilicity, as well as the dual and multiphilic descriptors are adequate for characterizing the global and local reactivity trends of the M(H2O)2A2 complex. It is found that the reactivity is well localized at the metallic center in M(H2O)2A2 and the dual descriptor (ΔfM(r)) can also be used to characterize the directional attack of the electrophile and nucleophile except for the selectivity of the reaction. On the basis of the values of ωM and Δsk, and the sign of ΔfM(r), the selectivity of the nucleophilic reagent (R(-)) for M(II) in M(H2O)2A2 (from high to low) follows this order: Cu(II) > Ni(II) > Co(II) > Fe(II) ≫ Mn(II) > Zn(II) > Cr(II). The Lewis base (A(-)) improves chemical reactivity and selectivity because of changing the reaction path and forming an intermediate, which possesses the higher antibonding character and the larger HOMO/LUMO gap. NBO or AIMALL analysis and Frontier orbital theory results presented here provided more theoretical support for the above reactivity and selectivity studies.