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Bioactive peptides are short amino acid sequences that play important roles in various physiological processes, including antioxidant and protective effects. These compounds can be obtained through protein hydrolysis and have a wide range of potential applications in a variety of areas. However, despite the potential of these compounds, more in-depth knowledge is still necessary to better understand details regarding their chemical reactivity and electronic properties. In this study, we used molecular modeling techniques to investigate the electronic structure of isolated amino acids (AA) and short peptide sequences. Details on the relative alignments between the frontier electronic levels, local chemical reactivity and donor-acceptor properties of the 20 primary amino acids and some di- and tripeptides were evaluated in the framework of the density functional theory (DFT). Our results suggest that the electronic properties of isolated amino acids can be used to interpret the reactivity of short sequences. We found that aromatic and charged amino acids, as well as Methionine, play a key role in determining the local reactivity of peptides, in agreement with experimental data. Our analyses also allowed us to identify the influence of the relative position of AA and terminations on the local reactivity of the sequences, which can guide experimental studies and help to propose/evaluate possible mechanisms of action. In summary, our data indicate that the position of active sites of polypeptides can be predicted from short sequences, providing a promising strategy for the synthesis and bioprospection of new optimized compounds., Competing Interests: Declarations. Competing interests: The authors have no competing interests to declare that are relevant to the content of this article., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

A major part of chemical conversions is carried out in the fluid phase, where an accurate modeling of the involved reactions requires to also take into account solvation effects. Implicit solvation models often cover these effects with sufficient accuracy but can fail drastically when specific solvent-solute interactions are important. In those cases, microsolvation, i.e., the explicit inclusion of one or more solvent molecules, is a commonly used strategy. Nevertheless, microsolvation also introduces new challenges-a consistent workflow as well as strategies how to systematically improve prediction performance are not evident. For the COSMO and COSMO-RS solvation models, this work proposes a simple protocol to decide if microsolvation is needed and how the corresponding molecular model has to look like. To demonstrate the improved accuracy of the approach, specific application examples are presented and discussed, i.e., the computation of aqueous pK a values and a mechanistic study of the methanol mediated Morita-Baylis-Hillman reaction.

A novel series of the 2-pyridine substituted 3a-e and 4-pyridine substituted 4a-e thiazole derivatives were synthesized, characterized, and evaluated for the biological activity. Crystallographic parameters and inter- and intramolecular interactions of 3a and 3c single crystals were examined through XRD analysis. The chemical reactivity potentials of the compounds were evaluated, by comparing with a theoretical approach based on DFT. The biological activity properties of synthesized compounds were determined by antimicrobial activity with Gram positive, Gram negative, Yeast via minimal inhibitory concentration (MIC) method and DNA cleavage activity studies. The most obvious findings to emerge from this study are that on the basis of both biological activity and chemical reactivity 4-pyridine thiazole hybrid compounds 4a-e showed more potent activity than 3a-e. In general, the antimicrobial activity of synthesized compounds follows the Bacillus cereus > Staphylococcus aureus > Candida albicans > Escherichia coli > Pseudomonas aeruginosa. The most potent compound 4c (MIC values 0.02 mM) exhibited antimicrobial activity against Staphylococcus aureus and Bacillus cereus. Furthermore, this compound has a good electrophilicity index value (4.56 eV)., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The MN12SX density functional, in connection with the Def2TZVP basis set, was assessed, together with the SMD solvation model (Solvation Model based on the Density), for calculation of the molecular properties and structure of a group of peptides of marine origin named Mirabamides A⁻H. All the chemical reactivity descriptors for the systems were calculated via Conceptual Density Functional Theory (CDFT). The active sites suitable for nucleophilic, electrophilic, and radical attacks were chosen by linking them with the Fukui function indices, nucleophilic and electrophilic Parr functions, and condensed Dual Descriptor Δ f ( r ) , respectively. Additionally, the p K a values for the different peptides are predicted with great accuracy as well as the ability of the studied molecule in acting as an efficient inhibitor of the formation of Advanced Glycation Endproducts (AGEs), which constitutes a useful knowledge for the development of drugs for fighting Diabetes, Alzheimer and Parkinson diseases. Finally, the bioactivity scores for the Mirabamides A⁻H are predicted through different methodologies.

Fukui functions are related to electron densities, and their interpretation permits the determination of reactivity of atomic centres. However, negative values cannot be interpreted by an "electron density based" model and represent a phenomenon that has been little investigated and understood. Previous works in the literature suggest that they are related to nodes in the wave function. In our investigations we can relate negative values to nitro groups and their position on aromatic systems, as it is a moiety with HOMO electron densities close to "0" related to "electron attracting" groups. This work can help us understand and predict this phenomenon and the associated chemical reactivities. We also pay attention to the influence of the nitro group angle vs. the aromatic ring. [ABSTRACT FROM AUTHOR]

Copyright of Baghdad Science Journal is the property of Republic of Iraq Ministry of Higher Education & Scientific Research (MOHESR) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Density functional theory (DFT) was used to study the mechanism of Diels–Alder (DA) reaction between 2‐Methyl‐ 1,3 Butadiene (MBD) with B12N12, B6N6C12 and B6C12N6 fullerens in the gas phase. In this mechanism, B‐N bonds of four‐membered and six‐membered rings of nanocages were chosen to react with MBD. Due to the existence of two types of B‐N bonds, two competitive pathways (a and b) were investigated. The effect of the substitution of carbon atoms instead of boron and nitrogen atoms on the stability of the structures and the regioselectivity of the DA reaction was examined. The potential energy of all structures and the activation barrier for all reaction pathways was evaluated. The chemical reactivity of fullerens using the molecular quantum descriptors was assessed. To evaluate the global electron density transfer in transition states (TS) structures, the natural bond orbital (NBO) analysis was performed. [ABSTRACT FROM AUTHOR]

Silymarin has been utilized as a traditional, complementary, and integrative medicine for centuries, despite a poor molecular‐level understanding of its interactions with other medicinal compounds and enzyme structures. However, recent studies indicate that this supplement, as with many others, should be considered with caution because it has the potential to interact with many drugs, medical plants, and foods. Silymarin is composed of several compounds that are either enantiomeric or have similar structures. Thus, this study presents the electronic structure properties and reactivity characteristics of silymarin components and warfarin through density functional theory modeling at the M06‐2X/6–311 + G(d,p) level of theory. The ligand‐protein interactions of the compounds with human serum albumin, cytochrome P450 (CYP2C9, CYP2C19, CYP2D6, and CYP3A4) enzymes, and alanine transaminase were presented using molecular docking. The critical residue‐based interactions of silymarin components and warfarin were fingerprinted. Furthermore, their drug‐likeness and toxicity characteristics were compared to those of warfarin and the well‐known flavonoids, taxifolin, and quercetin. The possibility of inhibiting the target enzymes to reduce the effectiveness of warfarin has been highlighted. [ABSTRACT FROM AUTHOR]

AbstractA novel heterocyclic compound named (Z)-5-(4-nitrobenzylidene)-3-N(3-chlorophenyl)-2-thioxothiazolidin-4-one (NCTh) was synthesized and analyzed using various techniques, including single crystal X-ray diffraction, FT-IR, UV-Vis, NMR spectroscopy, and mass spectral data methods. NCTh was observed to crystallize in the triclinic crystal system P-1 space group. To validate the experimental findings, density functional theory (DFT) calculations were performed using the B3LYP functional with the 6-311 G(d,p) basis set. The results indicated good agreement in geometrical parameters between the experimental and theoretical outcomes. The study also calculated HOMO-LUMO energies, molecular electrostatic potential (MEP), and global chemical reactivity descriptors to evaluate the compound’s reactivity. Additionally, the study conducted reduced density gradient and Hirshfeld surface analyses to reveal attractive, repulsive, and van der Waals strong and weak interactions. The calculation of thermodynamic parameters was also included. The study focused on investigating the nonlinear optical (NLO) properties of NCTh, which were characterized through key parameters such as the electric dipole moment (µ), polarizability (α), first-order hyperpolarizability (β), and second-order hyperpolarizability (γ). These properties provide insights into the material’s potential applications in optical and photonic technologies. Additionally, a molecular docking study was performed to further explore the structure-activity relationship, particularly in a biological context. The docking results revealed a strong ligand-protein interaction, with a binding energy of −10.3 kcal/mol, indicating significant affinity. Moreover, the inhibition constant (Ki) was calculated to be 0.0281 μM, suggesting a highly potent interaction, which could be relevant for drug design or biochemical applications. [ABSTRACT FROM AUTHOR]

The dissociation of methane is not only an important reaction step in catalytic processes, but also of fundamental interest. Dynamical effects during the dissociative chemisorption of methane on metal surfaces cause significant differences in computed reaction rates, compared to what is predicted by typical transition state theory (TST) models. It is clear that for a good understanding of the catalytic activation of methane dynamical simulations are required. In this paper, a general blueprint is provided for performing dynamical simulations of the dissociative chemisorption of methane on metal surfaces, by employing either the quasi-classical trajectory or ring polymer molecular dynamics approach. If the computational setup is constructed with great care-since results can be affected considerably by the setup - chemically accurate predictions are achievable. Although this paper concerns methane dissociation, the provided blueprint is, so far, applicable to the dissociative chemisorption of most molecules. [ABSTRACT FROM AUTHOR]

Benzophenone and its derivatives are widely used as UV filters and UV‐ink photoinitiators. The photoinitiating properties of benzophenones depend on their degree of conjugation and delocalization within the molecule. By understanding how conjugation, delocalization, and different substituents affect these properties, benzophenone derivatives can be customized for specific applications. Using quantum mechanical calculations based on B3LYP/6‐311++G(d, p) density functional theory (DFT), chemical reactivity, stability, and photoinitiating capabilities of 4‐(4‐methylphenylthio)benzophenone are analyzed. This includes studying its physical and chemical properties in the gas phase, as well as its excited state electronic transitions, vibrational characteristics, and spectroscopic properties both in gas phase and in various solvents. The DFT‐computed infrared spectra match experimental results. The UV/Visible spectra shows absorption towards longer wavelengths due to extended delocalization of π‐electrons. In different solvents with varying polarity, the absorption spectra exhibit high‐intensity peaks, shift in excitation energy and wavelengths based on the polarity of the solvent. This knowledge allows for the development of novel initiators with customized light absorption, excited state lifetimes, and reaction selectivities, which can enhance processes like UV‐curing, photopolymerization, and other light‐driven reactions. [ABSTRACT FROM AUTHOR]

The reactivity of 22 unsaturated molecules undergoing attack by a methyl radical (⋅CH3) have been elucidated using the condensed radical general‐purpose reactivity indicator (condensed radical GPRI) appropriate for relatively nucleophilic or electrophilic molecules. Using the appropriate radical GPRI equation for electrophilic attack or nucleophilic radical attack, seven different population schemes were used to assign the most reactive atoms in each of the 22 molecules. The results show that the condensed radical GPRI is sensitive to the population scheme chosen, but less sensitive than the radical Fukui function. Therefore, the reliability of these methods depends on the population scheme. Our investigation indicates that the condensed radical GPRI is most accurate in predicting the dominant products of the methyl radical addition reactions on a variety of unsaturated molecules when the Hirshfeld, Merz–Singh–Kollman, or Voronoi deformation density population schemes are used. Furthermore, for all populations schemes in the majority of instances where the radical Fukui function failed the radical GPRI was able to identify the most reactive atom under certain reactivity conditions. [ABSTRACT FROM AUTHOR]

Employing the formalism of the joint density functional theory (JDFT) in the grand canonical ensemble, this paper studies the electronic structure and relative reactivity of an hydroxyl radical adsorbed on the surface of three different metal oxides that share the rutile-type structure and the (110) crystal plane; these materials are electrodes used in electrochemical advanced oxidation processes which consist in the generation of hydroxyl radicals, highly reactive species, that are able to oxidize organic compounds to CO 2 , making these anodes efficient for wastewater treatment. By analyzing the changes in the average number of electrons as a function of the applied chemical potential at fixed external potential, we studied two reactivity indices from conceptual density functional theory: global and local softness, to help us understand the differences between these materials, additionally we propose a new scheme to approximate the redox properties of clean surfaces or surfaces in contact with different adsorbed molecules so that these values can be arranged in a relative potential scale which would allow direct comparison with experimental results. [ABSTRACT FROM AUTHOR]

Marine organisms have been found to produce compounds that have the potential to serve as templates for novel therapeutics. Among these compounds, peptides are of particular interest due to their intermediate size between amino acids and proteins. Kahalalides are a family of structurally complex cyclic peptides with potent cytotoxic and antitumor activities, making them promising candidates for cancer therapy. In this study, we investigate the chemical reactivity of Kahalalides A–F using Conceptual Density Functional Theory to gain insight into their bioactivity from a molecular perspective. Our investigation includes characterizing and isolating the peptides, determining their local and global properties and predicting the active reaction sites. We also calculate Bioactivity Scores to predict their biological targets. Overall, this study contributes to the discovery of new therapeutic peptides from natural sources by providing insights into their chemical reactivity and potential biological targets. [ABSTRACT FROM AUTHOR]

Using density-based quantities to establish a qualitative or even quantitative framework to predict molecular reactivity in density functional theory is of considerable interest in the current literature. Recent developments in information-theoretic approach (ITA) represent such a trend. Traditionally, we represent ITA quantities in terms of the electron density, shape function, and atoms in molecules. In this contribution, we expand the theoretical framework of ITA by introducing a new representation. To that end, we make use of the first-order partial derivative of ITA quantities with respect to the number of total electrons and then approximate them in the finite difference approximation. The new representation has both local (three-dimensional) and global (condensed to atoms) versions. Its close relationship with Fukui function from conceptual density functional theory was derived analytically and confirmed numerically. Extensions of our present approach to include other types of derivatives are discussed. This work not only enriches the theoretical framework of ITA with a new representation but also provides opportunities to expand its territory as well as the scope of its applicability in dealing with molecular processes and chemical reactivity from a new perspective. [ABSTRACT FROM AUTHOR]

• Novel organoammonium-Cd(II) hybrid material synthesized and characterized. • Crystal structure elucidated via X-ray diffraction and Hirshfeld analysis. • Crystal morphology predicted using Bravais-Friedel-Donnay-Harker (BFDH) model. • Optical, electronic properties explored experimentally and theoretically. • Chemical reactivity assessed with conceptual-DFT calculations. This study reports the synthesis and characterization of an organoammonium-cadmium(II) hybrid material, (BPH₂)₂[Cd₂Cl₈] (BP = 1-butylpiperazine), using a combination of experimental and theoretical techniques. Single-crystal X-ray diffraction shows a centrosymmetric crystal structure in the P 1 ¯ space group, featuring a zero-dimensional (0D) arrangement where binuclear [Cd₂Cl₈]⁴⁻ anions and (C₈H₂₀N₂⁺) cations are linked by N—H···Cl and C—H···Cl hydrogen bonds. Hirshfeld surface analysis further elucidates these intermolecular noncovalent interactions, highlighting the dominant role of H···Cl contacts in the molecular packing. The crystal morphology is further investigated via the Bravais-Friedel-Donnay-Harker (BFDH) model. Infrared (IR) spectroscopic analysis was conducted to identify vibrational modes, confirm structure, and elucidate bonding features. Additionally, Experimental UV–visible study indicates an optical band gap energy of 4.75 eV, and density functional theory (DFT) calculations corroborate these findings, predicting a direct band gap of 4.45 eV. Moreover, theoretical calculations, including the complex dielectric function, band structure, and total density of states (DOS), were performed to explore the electrical and optical properties. Finally, the chemical reactivity was evaluated using conceptual-DFT descriptors at the B3LYP/SDD/aug-cc-pVTZ level of theory. [Display omitted] [ABSTRACT FROM AUTHOR]

In this work, 2-thioxo -3 N-(2-ethoxyphenyl -5[4′-methyl -3′N-(2′-ethoxyphenyl) thiazol-2′(3′H)-ylidene] thiazolidin-4-one (E2Th2) was synthesized and its molecular structure determined by FT-IR, UV-Vis and NMR spectroscopic techniques along with a single crystal X-ray diffraction study. Quantum chemical calculations were performed to better understand its structural, spectroscopic and electronic properties such as HOMO and LUMO energy gap, MEP and global reactivity descriptors. Theoretical calculations were performed using density functional theory (DFT) based on the B3LYP/6-311G (d,p). Vibrational frequencies were assigned on the basis of PED and electronic transitions are calculated according to time-dependent density functional theory (TD-DFT). The HOMO and LUMO analysis are used to determine the charge transfer within the molecule. The NLO activity evaluation was based on the determination of the dipole moment, polarizability (α), first-order hyperpolarizability (β) and the second-order hyperpolarizability (γ) which were calculated using the same level of theory. The hyper-hardness descriptor (Γ) was explored and correlated with the NLO properties. Additionally, the stability of the molecule occurring from hyper-conjugative interaction, intramolecular hydrogen bond and charge delocalization were quantified using NBO analysis. The repulsive, attractive, and van der Waals strong and weak interactions were revealed by RDG and HS analyses. Finally, results have shown that the title compound can be used as attractive future NLO material. [ABSTRACT FROM AUTHOR]

Triphenylamine was used as a donor and electron-withdrawing groups in different positions as terminal acceptor groups in order to design a series of push–pull chromophores (D1-5). The dyes were characterized via UV–vis spectroscopy and electric, absorption, and thermal studies. Based on the theoretical results, the electrochemical and optical investigations of D1-5 displayed reduced bandgap HOMO–LUMO energies. In addition, these compounds exhibited an electrical character, making them promising donor dyes for solar cell usage. The B3LYP/6-31G (d, p) basis set using the density functional theory (DFT) was applied in this study. The second-order NLO response was also investigated for D1-5 chromophores. D1-5 compounds have higher second-order nonlinear characteristics and a smaller HOMO–LUMO gap than electron-accepting groups ranging from ultraviolet to near-infrared. The thermodynamic properties were also calculated as a function of temperature in the 298.15 K range, including heat capacity, entropy, enthalpy, free energy, and zero-point energy. [ABSTRACT FROM AUTHOR]

We consider SinCL-20 and GenCL-20 systems with carbon atoms replaced by silicon/germanium atoms and their dimers. The physicochemical properties of the silicon/germanium analogs of the high-energy molecule CL-20 and its dimers were determined and studied using density functional theory with the B3LYP/6-311G(d,p) level of theory. It was found that the structure and geometry of SinCL-20/GenCL-20 molecules change dramatically with the appearance of Si-/Ge-atoms. The main difference between silicon- or germanium-substituted SinCL-20/GenCL-20 molecules and the pure CL-20 molecule is that the NO2 functional groups make a significant rotation relative to the starting position in the classical molecule, and the effective diameter of the frame of the systems increases with the addition of Si-/Ge-atoms. Thus, the effective framework diameter of a pure CL-20 molecule is 3.208 Å, while the effective diameter of a fully silicon-substituted Si6CL-20 molecule is 4.125 Å, and this parameter for a fully germanium-substituted Ge6CL-20 molecule is 4.357 Å. The addition of silicon/germanium atoms to the system leads to a decrease in the binding energy. In detail, the binding energies for CL-20/Si6CL-20/Ge6CL-20 molecules are 4.026, 3.699, 3.426 eV/atom, respectively. However, it has been established that the framework maintains stability, with an increase in the number of substituting silicon or germanium atoms. In addition, we designed homodesmotic reactions for the CL-20 molecule and its substituted derivatives Si6CL-20/Ge6CL-20, and then determined the strain energy to find out in which case more energy would be released when the framework breaks. Further, we also studied the electronic properties of systems based on CL-20 molecules. It was found that the addition of germanium or silicon atoms instead of carbon leads to a decrease in the size of the HOMO–LUMO gap. Thus, the HOMO–LUMO gaps of the CL-20/Si6CL-20/Ge6CL-20 molecules are 5.693, 5.339, and 5.427 eV, respectively. A similar dependence is also observed for CL-20 dimers. So, in this work, we have described in detail the dependence of the physicochemical parameters of CL-20 molecules and their dimers on the types of atoms upon substitution. [ABSTRACT FROM AUTHOR]

< p>In this work, the interaction between Flutamide (FLU) anticancer drug with nucleobases such as cytosine, thymine, uracil, and adenine was studied by density functional theory (DFT) methods from a thermodynamic point of view. The Gibbs free energy (ΔG) and enthalpy (ΔH) of C-FLU, T-FLU, U-FLU and A-FLU complexes were computed and demonstrate that the stronger interaction between cytosine and FLU and the adsorption of the drug on the bases proceeds spontaneously. The negative value of ΔH indicates that the adsorption of FLU drug on the cytosine, thymine and uracil bases are exothermic, these results confirmed ΔE results. During the interaction of Flutamide drug with nucleobases, the energy levels of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) were significantly changed. The values of the energy gap (Eg) reduced during the adsorption of the FLU drug onto bases which confirmed that the reactivity of the resulted complex increase upon adsorption. On the other hand, as a result of theoretical calculations, the values of the Eg for the Base-FLU structures in water solution are decreased in comparison to the corresponding values in the gas phase, indicating more the reactivity of the studied complexes in the aqueous medium.

Small atomic clusters with exotic stability, bonding, aromaticity, and reactivity properties can be made use of for various purposes. In this work, we revisit the trapping of noble gas atoms (He–Kr) by the triatomic H3+ and Li3+ species by using some analytical tools from density functional theory, conceptual density functional theory, and the information-theoretic approach. Our results showcase that though similar in geometry, H3+ and Li3+ exhibit markedly different behavior in bonding, aromaticity, and reactivity properties after the addition of noble gas atoms. Moreover, the exchange–correlation interaction and steric effect are key energy components in stabilizing the clusters. This study also finds that the origin of the molecular stability of these species is due to the spatial delocalization of the electron density distribution. Our work provides an additional arsenal towards a better understanding of small atomic clusters capturing noble gases. [ABSTRACT FROM AUTHOR]

Surface hydroxylation has been extensively studied over the years for a variety of applications, and studies involving hydroxylation of different silica surfaces are still carried out due to the interesting properties obtained from those modified surfaces. Although a number of theoretical studies have been employed to evaluate details on the hydroxylation phenomenon on silica (SiO2) surfaces, most of these studies are based on computationally expensive models commonly based on extended systems. In order to circumvent such an aspect, here we present a low-cost theoretical study on the SiO2 hydroxylation process aiming to evaluate aspects associated with water-SiO2 interaction. Details about local reactivity, chemical softness, and electrostatic potential were evaluated for SiO2 model substrates in the framework of the density functional theory (DFT) using a molecular approach. The obtained results from this new and promising approach were validated and complemented by fully atomistic reactive molecular dynamics (FARMD) simulations. Furthermore, the implemented approach proves to be a powerful tool that is not restricted to the study of hydroxylation, opening a promising route for low computational cost to analyze passivation and anchoring processes on a variety of oxide surfaces. [ABSTRACT FROM AUTHOR]

Copyright of Erzincan University Journal of Science & Technology is the property of Erzincan Binali Yildirim Universitesi and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We review the early works which were precursors of the Conceptual Density Functional Theory. Starting from Thomas–Fermi approximation and from the exact formulation of Density Functional Theory by Hohenberg and Kohn's theorem, we will introduce electronegativity and the theory of hard and soft acids and bases. We will also present a general introduction to the Fukui functions, and their relation with nucleophilicity and electrophilicity, with an emphasis towards the importance of these concepts for chemical reactivity. [ABSTRACT FROM AUTHOR]

Reactivity descriptors indicate where a reagent is most reactive and how it is most likely to react. However, a reaction will only occur when the reagent encounters a suitable reaction partner. Determining whether a pair of reagents is well-matched requires developing reactivity rules that depend on both reagents. This can be achieved using the expression for the minimum-interaction-energy obtained from the density functional reactivity theory. Different terms in this expression will be dominant in different circumstances; depending on which terms control the reactivity, different reactivity indicators will be preferred.

Thermodynamic and kinetic components of density functional reactivity theory -based stabilization energies between interacting electron acceptors and electron donors are evaluated with and without taking into account perturbative effects on one reactant caused by the other. The values of the two energy components generated through these two approaches are then correlated to the Hammett's substituent constant σ through the relation σ = m log Δ E X Δ E H + b . Here Δ E X and Δ E H represent, respectively, energy components (either thermodynamic or kinetic) of the substituted and unsubstituted benzene derivatives. The generated data on six different series of reactions demonstrate that both perturbative and unperturbative approaches are of comparable reliability when either thermodynamic or kinetic energy components are used in the proposed relation, justifying the validity and generality of Hammett's free energy relation. [ABSTRACT FROM AUTHOR]

We provide a general (yet elementary) proof of Pearson's hard/soft acid/base principle. Contrary to previous attempts to justify this rule, we go beyond the venerable parabolic model of Parr and Pearson. This new treatment encompasses more realistic E versus N dependencies, while emphasizing the importance of the correct normalization of these models. [ABSTRACT FROM AUTHOR]

We investigate the rich stereochemistry of cocaine and its diastereoisomers from a theoretical perspective using density functional theory. The relative stability of the eight considered isomers is discussed, and a comparison of the corresponding internal coordinates is given. Our results reveal that the S-pseudococaine isomer is the most stable conformation, whereas the natural occurring isomer (R-cocaine) lies higher in energy. The different isomers' chemical reactivity is discussed based on the calculation of the hardness, softness, electrophilicity and dipole moment. It was found that the dipole moment varies over a broad range from 0.65 to 4.60 D, whereas the other properties are slightly modified. The solvent effect on the energy stability of the cocaine isomers was studied by considering chloroform, dimethyl-sulfoxide (DMSO) and water as implicit solvents. Our calculations show that the different isomers' energy order and their energy gaps are slightly modified due to solvent effects. However, in all cases, the S-pseudococaine remains the most stable isomer. However, the dipole moment and the chemical reactivity of the cocaine isomers increase with the solvent polarity. [ABSTRACT FROM AUTHOR]

Conventional drugs used to treat Tuberculosis (TB) are becoming ineffective due to the occurrence of multiple drug resistant strains of tuberculosis (TB). This has made the TB disease a a serious global health dilemma. Hence, there is desperate necessity for the advancement of new drugs. In this work, the chemical reactivity and bioactivity of several analogs ofpyrazinamide (PZA) were investigated. PZA is one of the first-line of drugs used to treat tuberculosis and is a key contributor to shortening the treatment time for the disease. Chemical reactivity descriptors of pyrazinamide (PZA) and its analogs of acetylsalicyclic acid and salicyclic acid were investigated using conceptual density functional theory in water as a solvent at the MN12SX/Def2TZVP level of theory. Results have shown that all PZA analogs have improved their global and local reactivity indeces as compared to pyrazinamide based on its electronegativity, electrodonating power, electroaccepting power, eletrophilicity, global hardness and dual descriptor condensed fukui indexes. Moreover, their pKa values are slightly higher than PZA. In terms of its drug-likeness, all PZA analogs passed the Lipinski's Rule of Five criteria. Furthermore, their bioactivity scores are significantly better than pyrazinamide indicating good reaction to G-Protein Coupled Receptor (GPCR) ligands, kinase inhibitors, ion channel modulators, nuclear receptor ligands, protease inhibitors and other enzyme targets. Overall, the PZA analogs are found to be promising anti-tuberculosis drugs. Based on global and local reactivity descriptors, pKa and bioactivity scores, PZA analog of 5-n-Octanoylsalicylic acid is the most reactive among the PZA analogs tested.

We discuss an extension of the venerable Parr‐Pearson parabolic charge transfer model that explicitly includes 3rd order effects. We then use this new model to provide new arguments supporting the validity of Parr and Yang's "|Δμ| big is good" (DMB) principle. Additionally, we show how to re‐derive this principle from the Parr‐Pearson parabolic model, using simpler arguments than those presented in our previous proof of the DMB rule. [ABSTRACT FROM AUTHOR]

In the present work, we study the new two dimensional materials with tunable bandgap and high chemical reactivity via locating the alkali metals and superalkalis (Li, Na, K, Li3O, Na3O, and K3O) on the graphdiyne (GDY) sheets with open hexagonal edges. Our density functional theory (DFT) calculations reveal that the bandgap energy of GDY with a different open zigzag or armchair edges (ZGDY and AGDY) is decreased by interacting with alkali metals and superalkali species. We found that the alkali metals and superalkalis lowered the bandgap energy of AGDY and ZGDY by more than 170% and converted them into the semimetals. Our results also show that the M3O/ZGDY systems show higher chemical reactivity as compared to the other studied systems. Among the studied M(M3O)/ZGDY(AGDY) systems, the maximum binding energy, maximum means static polarisability, minimum bandgap energy, and minimum chemical hardness are related to the K3O/ZGDY complex. Consequently, the K3O/ZGDY is a promising chemically reactive material for applications in various fields such as gas detectors, catalysts in the oxygen reduction reactions, and drug delivery application. [ABSTRACT FROM AUTHOR]

Effects of substituent groups on aqueous solubility, chemical reactivity and absorption wavelength of Disperse red 73 (DR73) were theoretically investigated using density functional theory (DFT) method. This study is in view of introducing new monoazo disperse dyes with improved aqueous solubility, absorption behaviour, and degradation tendency. Aqueous solubility was calculated using Cramer et al. solubility equation and the parameters used were obtained using conductor-like screening model for realistic solvation (COSMO-RS). Chemical reactivity and catalytic affinity were evaluated using some molecular orbital dependent reactivity descriptors. Susceptibility of the molecules to radical attacks was predicted using Fukui functions. Absorption wavelength was calculated using the B3LYP functional with the 6-31G* basis set. The results showed that electron withdrawing −CN substituent promoted aqueous solubility of DR73 more than the −NO2 counterpart, while the solubility is mostly enhanced by −NH2 substituent compared to the other electron donating groups studied. Most of the derivatives yielded longer absorption wavelength in the visible region and are chemically less stable (i.e. more degradable) compared to the parent molecule. Among the photocatalysts considered, ZnO is predicted as the most efficient candidate for degradation of the dyes. Predicted properties showed remarkable sensitivity to substitution positions in the parent molecule. [ABSTRACT FROM AUTHOR]

Isopimpinellin (C13H10O5), alternative name 5,8-dimethoxypsoralen, is one of the furocoumarin compounds. This traditional Chinese medicine extract has attracted a great deal of attention in recent years due to its pharmacological properties, especially its antifungal effect. The main purpose of this study was to study the molecular structure and chemical reactivity of isopimpinellin using the density functional theory method. To understand and interpret the reactivity of isopimpinellin, various chemical reactivity descriptors such as chemical potential (µ), electronegativity (ɰ), chemical hardness (ɳ) and electrophilicity (w) and local reactivity index condensed Fukui function (fi(r)) have been calculated with five hybrid functionals PBE1PBE, MPW1PW91, B3LYP, X3LYP and B3PW91. These chemical reactivity descriptors indicate that the isopimpinellin molecule has a good antioxidant activity, which could be one of the reasons for its action as an effective antifungal drug. The condensed Fukui functions of isopimpinellin molecule provide a complete scheme of chemical reactivity of one molecule. [ABSTRACT FROM AUTHOR]

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Density functional theory (DFT) is used for investigating the electronic structure and optical properties carbon nanotubes (CNTs) with doped B, Al, Ga, Si, Ge, N, P and As and different diameters. Our results show that the stability of CNTs increased when it comes to an increase in diameter, however, stability decreases depending on doping additives to pure CNTs. B-doped CNTs are the most effective for electronic conductivity due to its lower band gap. The non-linear optical (NLO) properties are discussed according to dipole moment, polarizability, and hyperpolarizability. All the doped CNTs exhibit a good NLO activity. B-, Al-, Ga- and N -doped CNTs have a significant effect on NLO properties. The band gap of CNTs considerably decreased from 2.76 eV to 1.40 eV and 1.78 eV–0.83 eV based on the diameter. The reactivity properties investigated based on chemical hardness, softness, and potential, electronegativity, electrophilicity, the maximum amount of electronic charge index, the electron accepting and donating capability as well as electronic density of states are also presented and analyzed. Herein, the results indicated that the characteristic properties of CNTs can be controlled with different atoms doped CNTs and diameters. • The analyses of the energetic of pure and doped CNTs are investigated in detail. • The electronic and reactivity properties of pure and doped CNTs are compared. • The characteristic properties of CNTs can be controlled based on doped atoms. • B-doped CNTs have desirable electronic conductivity. [ABSTRACT FROM AUTHOR]

• Computational and experimental work has been performed on cocrystal of hydrochlorothiazide (HCTZ) and nicotinamide (NCT). • H-bonding interaction was studied by using monomeric, dimeric and trimeric models of HCTZ-NCT cocrystal. • NH 2 and C = O groups were involved in neighbouring hydrogen bonding interactions. • QTAIM and NBO analysis were done to explore inter and intramolecular H-bond interactions. • MEPS was performed to observe the reactive sites of the molecules. The present work focuses on the study of structural, vibrational, chemical properties and the effect of hydrogen bonding interaction in the formation of a cocrystal of hydrochlorothiazide (HCTZ, a diuretic drug) with nicotinamide (NCT) using vibrational spectroscopy (FT-IR and FT-Raman) and density functional theory. HCTZ being a BCS class IV drug, has low permeability and solubility; therefore, its cocrystal is studied. Monomer, dimer and trimer of HCTZ-NCT cocrystal were studied to understand hydrogen bonding interactions. The shifting in the wavenumber and the elongation in bond lengths of the amide (NH 2) group of HCTZ and carbonyl (C = O) group of NCT were observed in all the models of HCTZ-NCT cocrystal due to the hydrogen bonding interaction. The importance of hydrogen bonding were also explored by natural bond orbital (NBO) analysis in support of the quantum theory of atom in molecules (QTAIM). The chemical reactivity of HCTZ, NCT and HCTZ-NCT cocrystal was examined by MEPS map, FMOs, global electronic reactivity descriptor, ECT descriptors, and molar refractivity. The lesser value of the HOMO-LUMO energy gap in the cocrystal than API reflects that the chemical reactivity of the cocrystal was better than API itself. The comparison between API(HCTZ) and cocrystal (HCTZ-NCT) implies that pharmaceutical cocrystals may be a better option to improve and enhance the pharmacological properties of drugs. [Display omitted] [ABSTRACT FROM AUTHOR]

In this paper, the antiestrogenic properties of Tamoxifen analogs have been investigated and a theoretical report of its analogs interaction with the pocket site of some hormone receptors are presented. Analogs were generated by modification of the hydrophilic functional group of Tamoxifen by hydroxyl, amide, carboxyl, and sulfhydryl functional groups, in an attempt to improve their activity and selectivity. The analogs exhibit a negative binding energy in the estrogen and progesterone receptors, which indicates a spontaneous interaction between the analogs and the pocket site in the hormone receptors. The values of the molecular polar surface area indicate that the analogs have good permeability and are strong electrophiles. The couplings showed electrostatic interactions such as hydrogen bond and π-π interactions. According with the Lipinsky Rule of Five, the four analogs presented a good biodistribution, permeability, and pharmacological action on the hormone receptors. The analysis of the charge transfer suggests a limited enhanced oxidative damage in the estrogen receptor that not takes place with the progesterone receptor.

Rationalisation of computational results towards appreciating and predicting chemical reactivity is a topic worthy of investigation in theoretical chemistry. In this regard, a robust and generally applicable framework to comprehend the problem is still lacking. Nevertheless, on the basis of a density functional theory (DFT) energy partition scheme where the total electronic energy is decomposed into three independent effects as steric, electrostatic and the fermionic quantum, the fundamental driving forces of chemical processes to understand molecular reactivity have recently been proposed. In the present contribution, the two related descriptors, electrostatic and steric forces, are utilised to evaluate their applicability and accountability to comprehend different chemical reactivity properties. To do so, we have considered the electrophilic and nucleophilic regioselectivity, stereoselectivity and etherification reaction of phenolic derivatives as illustrative examples of reactivity-related phenomena. Highlighting the distinguished characteristics of the descriptors under study, their usefulness for analysing the chemical reactivity properties and reproducing experimental evidences is showcased. On the whole, our findings corroborate that the DFT energy partitioning scheme and the associated reactivity descriptors can pave the way towards theoretical rationalisation of chemical reactivity-related phenomena. [ABSTRACT FROM AUTHOR]

Abstract In the present study, a combined theoretical and experimental approach is used to study the structure and properties of 4-methoxydalbergione (MD). The optimized geometry was calculated by B3LYP method using 6–311++G(d,p) basis set. Three conformers of MD (MD I, MD II and MD III) have been found by potential energy surface scan. The FT-Raman and FT-IR spectra were recorded in the solid phase, and interpreted in terms of potential energy distribution analysis. Good consistency is found between the calculated results and observed spectra. The detailed interpretation of electron delocalization from filled lone pair orbitals to unfilled antibonding molecular orbitals of most interacting molecular orbitals of the molecule has been done by natural bond orbital (NBO) analysis. HOMO-LUMO energy gap shows that chemical reactivity of MD II is higher than MD I and MD III. Molecular electrostatic potential (MEP) surface has also been predicted with the help of density functional theory. Global and local reactivity descriptors are used to study the chemical reactivity of the molecule. Chemical reactivity parameters show that MD II is softer and chemically more reactive than MD I and MD III. Topological parameters at bond critical points (BCP) have been evaluated by 'Quantum theory of atoms in molecules' (QTAIM). The docking studies revealed that the active sites C=O of MD showed best binding energies of −5.17, −5.43, −4.31,-4.77, −5.86 and −4.77for 5O3L, 1HTM, 3UV5, 5I1Q, 1MU7 and 1QZQ respectively, which are bacterial proteins of Escherichia coli. Graphical abstract Image 1 Highlights 1. Molecular structure and vibrational analysis of 4-methoxydalbergione (MD) were presented using FT-IR and FT- Raman spectroscopy and quantum chemical calculations. 2. The UV–Visible absorption spectrum was examined in DMSO solvent and compared with one calculated in gas phase as well as in solvent environment. 3. HOMO-LUMO energy gap shows that chemical reactivity of MD. 4. Natural Bond Orbital (NBO) analysis is followed to figure out the stability of the molecule 5. Investigation of ligand-protein interaction, molecular docking simulations has also been done on bacterial proteins. [ABSTRACT FROM AUTHOR]

In this work, optimised structures, structural and spectroscopic properties of 2,2ʹ-dipyridylamine (DPA) in solvent media have been investigated. Conformational structures of DPA were determined and relative population distributions of the conformations were obtained. Vibrational modes were calculated for each environment and they were compared with the experimental values. The effects of the changing solvent environments on the molecular structures were investigated and hydrogen bonded complex structures that DPA could form with water molecules were studied. As a result of this study, the effects of solvent environments on the molecular structure of DPA have been determined. Chemical reactivities of DPA which have not been studied previously have been determined. When the solid phase infrared spectrum of pure DPA was examined, it was seen that N-H stretching mode was observed at 3250 cm−1. Since it will mean that there is bonded N-H in the structure, the dimer structure of DPA has been investigated. [ABSTRACT FROM AUTHOR]

Two analog acids, once is phosphonic acid, 3-Oxo-3- p -tolylpropylphosphonic acid, and the other is carboxylic acid, 4-Oxo-4-p-tolyl-butyric acid have been studied from a theoretical point of view in order to know their electronic, vibrational and thermodynamic properties by means of Density Functional Theory (DFT) calculations. The stable structures were optimized by using the hybrid B3LYP/6-31G method. The different proprieties for both compounds were analysed by means of the HOMO-LUMO proprieties, atomic charges, dipole moments, molecular electrostatic potentials and thermodynamic parameters. The vibrational spectra of the two acids are calculated and compared with those obtained with experimental FTIR method. The reactivity of molecules using various descriptors such us local softness, electrophilicity, electronegativity, hardness, HOMO-LUMO gap etc. are calculated and discussed. [ABSTRACT FROM AUTHOR]

Abstract: Optimized molecular structures and total energies of 3-fluoro-, 3-chloro-, 3-bromopyridine (3‑FP, 3-CP, and 3-BP) molecules in vacuum, benzene, toluene, chloroform, dichloromethane, ethanol, dimethylsulfoxide and water media were investigated using DFT/B3LYP-6311++G(d,p) method. Moreover, in order to be able to see the effects of changing physical conditions, the thermochemical properties of the structures have been calculated in different temperatures and solvent media. Vibrational frequencies of 3-FP, 3-CP, and 3-BP molecules in vacuum and solvent media were calculated and compared to experimental data from the literature. Also, the chemical reactivities of the structures were calculated from HOMO-LUMO energies. Molecular electrostatic potential maps were plotted and atomic charges of each atom were determined. As a result of the study, it was determined that the molecular parameters of these three structures were slightly influenced by the changing solvent polarity, but the vibration frequencies and other chemical properties have very seriously affected. [ABSTRACT FROM AUTHOR]

Three different DFT methods, B3LYP, M06-2X and M06, with PCM (polarized continuum model) solvent environment were performed to study the binding of Ca 2+ with different groups of superplasticizers. Small monomers contained one or two groups, respectively, called as phosphonate, phosphate, carboxylate, sulfonate, sulfate and alkoxide were selected as theoretical models. The stable binding conformations of Ca 2+ with monomers containing a single group optimized by the three DFT methods are similar and the binding strength follows the order, phosphonate ≈ phosphate > carboxylate > sulfonate ≈ sulfate > alkoxide ≈ water. The chemical reactivity and the electrophilic attack, not the natural atomic charges, of those monomers contribute significantly to the binding strength with Ca 2+ . The stable conformations of monomers containing two groups binding with Ca 2+ are complex and the structures of the complexes by the three DFT methods are different for the phosphonate and phosphate. However, the order of the binding energies of those monomers with calcium ions calculated by the three DFT method are consistent and also agree with that of the monomers containing a single group. The values of the binding energies are two times more than the binding energies of the monomers containing single group. [ABSTRACT FROM AUTHOR]

The stabilities and reactivities of two transition metal (, Zn)-doped structures of C fullerene have been investigated by density functional theory approach. We have observed a noticeable structural change in pristine C due to the substitution of one of its carbon atom by Cu or Zn atom. From our findings, it is found that the energy gap of CCu and CZn increases with respect to pristine C, thus making the two doped fullerenes more stable than their pristine counterpart. The reactivity parameters such as chemical hardness, chemical potential and electrophilicity index for these structures are also studied. Interestingly, our calculations reveal that both the doped fullerenes obey the maximum hardness principle and minimum electrophilicity principle. Also, from the electronic absorption spectra analysis, it can be inferred that the maximum absorption peak of the two heteroatom-substituted fullerenes CCu and CZn are shifted towards the longer wavelength region as compared to the pure C fullerene, which clearly indicates that a red shift is introduced on account of doping. [ABSTRACT FROM AUTHOR]

This study assessed eight density functionals that include CAM-B3LYP, LC- ω PBE, M11, MN12SX, N12SX, ω B97, ω B97X, and ω B97XD related to the Def2TZVP basis sets together with the SMD solvation model. These are assessed in calculating the molecular properties and structure of the Blue-M1 intermediate melanoidin pigment. Notably, the chemical reactivity descriptors for the system are calculated via the Conceptual Density Functional Theory. The choice of active sites applicable to nucleophilic, electrophilic as well as radical attacks is made by linking them with Fukui functions indices, electrophilic Parr functions, and condensed dual descriptor Δ f ( r ) . The predicted maximum absorption wavelength tends to be considerably accurate relative to the experimental value. The study found the MN12SX and N12SX density functionals to be the most appropriate in predicting the chemical reactivity of the molecule under study. [ABSTRACT FROM AUTHOR]

In this work, we have synthesized new coumarin Schiff base molecule, viz., 6-(4- n -heptyloxybenzyoloxy)-2-hydroxybenzylidene)amino)-2H-chromen-2-one and characterized its structural, electronic and spectroscopic properties experimentally and theoretically. The theoretical analysis of UV–visible absorption spectra reflects a red shift in the absorption maximum in comparison to the experimental results. Most of the vibrational assignments of infrared and Raman spectra predicted using density functional theory approach match well with the experimental findings. Further, the chemical reactivity analysis confirms that solvent highly affects the reactivity of the studied compound. The large hyperpolarizability value of the compound concludes that the system exhibits significant nonlinear optical features and thus, points out their possibility in designing material with high nonlinear activity. [ABSTRACT FROM AUTHOR]

Previously, theoretical studies for 2,6-lutidine/BR 3 (R = F, Me, C 6 F 5 ) (J. Phys. Chem. A, 2010) and PR 3 /B(C 6 F 5 ) 3 (R = Me, Ph, tBu, C 6 F 5 ) (Chem. Phys. Lett., 2012) pairs have been carried out by us to fully understand the reactivity differences between classical Lewis adducts and frustrated Lewis pairs (FLPs). Fukui function, as a conceptual DFT-based reactivity descriptor, was calculated and shown to explain well the observed reactivity of these Lewis pairs. The initially promising results encouraged us to focus on the reactivity for a huge number of published FLPs by using other conceptual DFT-based reactivity descriptors. In this work, various descriptors were used to understand the intermolecular and intramolecular Lewis centers’ reactivities of FLPs. The calculated results shown that, although there are a few exceptions, the adducts and “frustrated complex” of nonreactive pairs and reactive pairs are characterized by the opposite reactivity descriptors. The reactivity of Lewis pairs evaluated by reactivity descriptors also achieves some thermodynamic support from the Gibbs free energies of H 2 activation. [ABSTRACT FROM AUTHOR]

We perform a theoretical study on a set of carbon nanorings (CycloParaPhenylenes or CPP) envisioned as molecular templates for the selective synthesis of carbon nanotubes. The shape of these precursors, originating from bending n phenylene units in para position until forming the corresponding nanoring [ n ]CPP, may drive the growth of armchair single-walled nanotubes. This kinetic and thermodynamic study covers a set of molecules with different diameters, analyzing the exothermicity and the reaction path of a CPP-based radicaloid mechanism. The methodology employed is based on validated density functionals for mechanistic studies, shedding light on the viability of this synthetic pathway. [ABSTRACT FROM AUTHOR]

The electronic structure and the participation of the simplest azomethine imine (AI) in [3+2] cycloaddition (32CA) reactions have been analysed within the Molecular Electron Density Theory (MEDT) using Density Functional Theory (DFT) calculations at the MPWB1K/6-311G(d) level. Topological analysis of the electron localisation function reveals that AI has a pseudoradical structure, while the conceptual DFT reactivity indices characterises this three-atom-component (TAC) as a moderate electrophile and a good nucleophile. The non-polar 32CA reaction of AI with ethylene takes place through a one-step mechanism with moderate activation energy, 8.7 kcal·mol-1. A bonding evolution theory study indicates that this reaction takes place through a non-concerted [2n + 2] mechanism in which the C-C bond formation is clearly anticipated prior to the C-N one. On the other hand, the polar 32CA reaction of AI with dicyanoethylene takes place through a two-stage one-step mechanism. Now, the activation energy is only 0.4 kcal·mol-1, in complete agreement with the high polar character of the more favourable regioisomeric transition state structure. The current MEDT study makes it possible to extend Domingo's classification of 32CA reactions to a new pseudo(mono)radical type (pmr-type) of reactivity. [ABSTRACT FROM AUTHOR]

The present study emphasizes on structural, opto-electronic, vibrational, and nonlinear properties, at the electronic structure level, on the 4-fluoro-4-hydoxybenzophenone molecule using the first principles calculation. Detailed vibrational assignments of the wavenumbers are carried out on the basis of potential energy distribution and a good agreement between the reported and calculated wavenumbers has been observed. Furthermore, the molecular electrostatic potential surface predicts the reactive site of the molecule. From the time dependent density functional theory analysis of UV-visible spectra, a red shift has been observed at the maximum absorption wavelength when the gaseous medium is replaced by a solvent medium. The 4-fluoro-4-hydroxybenzophenone molecule possesses large hyperpolarizability value which implies its usefulness in nonlinear optical applications. [ABSTRACT FROM PUBLISHER]