LANL2DZ basis sets recontracted in the framework of density functional theory

Development of novel organometallic sulfonamides with N-ethyl or N-methyl benzenesulfonamide units as potential human carbonic anhydrase I, II, IX and XII isoforms' inhibitors: Synthesis, biological evaluation and docking studies

In the search of new cymantrenyl- and ferrocenyl-sulfonamides as potencial inhibitors of human carbonic anhydrases (hCAs), four compounds based on N-ethyl or N-methyl benzenesulfonamide units have been obtained. These cymantrenyl (1a-b) and ferrocenyl (2a-b) derivatives were prepared by the reaction between aminobenzene sulfonamides ([NH2-(CH2)n-(C6H4)-SO2-NH2)], where n = 1, 2) with cymantrenyl sulfonyl chloride (P1) or ferrocenyl sulfonyl chloride (P2), respectively. All compounds were characterized by conventional spectroscopic techniques and cyclic voltammetry. In the solid state, the molecular structures of compounds 1a, 1b, and 2b were determined by single-crystal X-ray diffraction. Biological evaluation as carbonic anhydrases inhibitors were carried out and showed derivatives 1b y 2b present a higher inhibition than the drug control for the Human Carbonic Anhydrase (hCA) II and IX isoforms (KI = 7.3 nM and 5.8 nM, respectively) and behave as selective inhibition for hCA II isoform. Finally, the docking studies confirmed they share the same binding site and interactions as the known inhibitors acetazolamide (AAZ) and agree with biological studies.

J P, Harohally NV, Krishnamurthy C, Jathi K, Ahmad A, Alshammari MB, Lokanath NK. Structural Investigation of Schiff Base Ligand and Dinuclear Copper Complex: Synthesis, Crystal Structure, Computational, and Latent Fingerprint Analysis

The structural studies of the fluorinated Schiff base ligand and its copper complex were synthesized and characterized by Fourier transform infrared, UV-visible, and photoluminescence spectroscopy. Single-crystal X-ray diffraction analysis unveils a dinuclear copper complex arising from double bridging acetate anions to copper ions that are chelated by the tridentate Schiff base ligand Cu(LS). The trigonality index τ5 of 0.080 indicates a distorted square pyramidal coordination geometry for the metal. The SL ligand and complex exhibit intra- and intermolecular interactions, leading to unique supramolecular architectures. The structural changes between the free halogenated Schiff base ligand and upon coordination with the metal were extensively studied by experimental and theoretical approaches. The intra- and intermolecular interactions have been analyzed by Hirshfeld surface and quantum theory of atoms in molecules analysis, and the enrichment ratio highlights the most favored interactions in the formation of molecular packing. The chemical and physical properties, such as the HOMO - LUMO energy gap, chemical reactivity, and electron density topology, are studied using density functional theory studies. In addition, the Schiff base ligand compound is used to study the latent fingerprint analysis.

Biological regulatory network analysis for targeting the mitochondrial calcium uniporter (MCU) mediated calcium (Ca2+) transport in neurodegenerative disorders

Calcium (Ca2+) has been observed as the most important ion involved in a series of cellular processes and its homeostasis is critical for normal cellular functions. Mitochondrial calcium uniporter (MCU) complex has been recognized as the most important calcium-specific channel located in the inner mitochondrial membrane and is one of the major players in maintaining the Ca2+ homeostasis by transporting Ca2+ across the mitochondrial membrane. Furthermore, dysregulation of the mitochondrial Ca2+ homeostasis has been orchestrated to neurodegenerative response. This necessitates quantitative evaluation of the MCU-dependent mROS production and subsequent cellular responses for more specific therapeutic interventions against neurodegenerative disorders. Towards this goal, here we present a biological regulatory network of MCU to dynamically simulate the MCU-mediated ROS production and its response in neurodegeneration. Previously, ruthenium complex RuRed and its derivatives have been reported to show low nM to high µM potency against MCU to maintain cytosolic Ca2+ (cCa2+) homeostasis by modulating mitochondrial Ca2+ (mCa2+) uptake. Therefore, structural modeling and dynamic simulation of MCU pore-forming subunit is performed to probe the interaction profiling of previously reported Ru265 and its derivatives compounds with MCU. The current study highlighted MCU as a potential drug target in neurodegenerative disorders. Furthermore, ASP261 and GLU264 amino acid residues in DIME motif of MCU pore-forming subunits are identified as crucial for modulating the activity of MCU in neurodegenerative disorders.

5-Aminoisophthalate-based kojic acid-appended bis-1,2,3-triazole: a fluorescent chemosensor for Cu2+ sensing and in silico study

A new, easy-to-prepare, and highly selective fluorescent chemosensor, i.e., 5-aminoisophthalate-based kojic acid-appended bis-1,2,3-triazole, was synthesized from an alkyne of 5-aminoisophthalic acid and azido-kojic acid using Cu(i)-catalyzed click chemistry and then successfully characterized. The alkyne structure of 5-aminoisophthalic acid, 1, was supported by the single-crystal X-ray crystallographic data. The fluorescent probe 3 was found to be highly selective for Cu2+ ions supported by the Job's plot with a stoichiometric ligand : metal ratio of 2 : 1, exhibiting almost a two-fold enhancement in the emission intensity upon the addition of Cu2+ ions (0-25 μM) with a detection limit of 8.82 μM. A comparison with LODs from previously developed chemosensors for Cu2+ ions was also conducted. Reversibility analysis indicated that probe 3 could be used as both a reusable sensor and as a scavenger of copper ions. DFT calculations with the basis sets B3LYP/6-311G(d,p) and LanL2DZ were employed for geometrical optimizations of structures of the alkyne 1, azide 2, probe 3, and complex 3.Cu2+. Hirshfeld surface analysis revealed significant intermolecular interactions in compound 1. Additionally, molecular docking for the antimicrobial activity showed the better antibacterial efficacy of probe 3.

Molecular Copper(I)-Sensitized Photoanodes for Alcohol Oxidation under Ambient Conditions

Dye-sensitized photoelectrochemical cells can enable the production of molecules currently accessible through energetically demanding syntheses. Copper(I)-based dyes represent electronically tunable charge transfer and separation systems. Herein, we report a Cu(I)-bisdiimine donor-chromophore-acceptor dye with an absorbance in the visible part of the solar spectrum composed of a phenothiazine electron donor, and dipyrido[3,2-a:2',3'-c]phenazine electron acceptor. This complex is incorporated onto a zinc oxide nanowire semiconductor surface effectively forming a photoanode that is characterized spectroscopically and electrochemically. We investigate the photo-oxidation of hydroquinone, and the photosensitization of 2,2,6,6-tetramethylpiperidine-1-oxyl and N-hydroxyphthalimide for the oxidation of furfuryl alcohol to furfuraldehyde, resulting in near quantitative conversions, with poor selectivity to the alcohol.

Substitution Effects in Aryl Halides and Amides into the Reaction Mechanism of Ullmann-Type Coupling Reactions

In this article, we present a comprehensive computational investigation into the reaction mechanism of N-arylation of substituted aryl halides through Ullmann-type coupling reactions. Our computational findings, obtained through DFT ωB97X-D/6-311G(d,p) and ωB97X-D/LanL2DZ calculations, reveal a direct relation between the previously reported experimental reaction yields and the activation energy of haloarene activation, which constitutes the rate-limiting step in the overall coupling process. A detailed analysis of the reaction mechanism employing the Activation Strain Model indicates that the strain in the substituted iodoanilines is the primary contributor to the energy barrier, representing an average of 80% of the total strain energy. Additional analysis based on conceptual Density Functional Theory (DFT) suggests that the nucleophilicity of the nitrogen in the lactam is directly linked to the activation energies. These results provide valuable insights into the factors influencing energetic barriers and, consequently, reaction yields. These insights enable the rational modification of reactants to optimize the N-arylation process.

Investigation of the interaction of thymine drugs with Be12O12 and Ca12O12 nanocages: A quantum chemical study

Based on the DFT in a Wb97xd/6-311+G* level of theory, the interaction of thymine derivatives with Be12O12 and Ca12O12 nanocages was investigated. It was found that adsorption energies of thymine molecules on the Be12/Ca12-O12 surface was around -43.16, -60.06 and -29.62, -50.71, -45.95, -30.27 kcal/mol, for thymine (TH1), 1-amino thymine (TH2) and thymine glycol (TH3), respectively and this result supported the drug's adsorption. Additionally, according to the FMOs and MEP studies, a charge transfer from TH's to nanocages. Additionally, both molecular orbitals demonstrate that the LUMO and HOMO are primarily found on the BeO's surface.

DFT Study on the Spin States of Polyaniline-3d Transition-Metal (Sc-Zn) Composites and Their Sensing Application to Detect Chemical Warfare Agents

Organic-inorganic composite materials, combining polymers with transition metal (TM) atoms based on PAni and 3d TMs, have been designed and investigated in various spin states by performing density functional calculations. These designed composites were analyzed for their stability in different spin states as well as for their calculated electronic properties, including binding energies, frontier molecular orbitals, and dipole moments. Additionally, 3D isosurfaces and 2D scattered plots of reduced density gradient as a function of (sign λ2)ρ provide insights into the noncovalent interactions between the composite units. The most stable Mn@PAni composite has been assessed as a sensing material for chemical warfare blood agents (HCN, NCCl, NCBr, NCCN, and AsH3) using density functional-based calculations. The reduced band gap and significant red/blue shift in the UV-vis spectra obtained through TDDFT calculations underline the selectivity and efficiency of the Mn@PAni composite toward different analytes.

A density functional theory study on the adsorption of Mercaptopurine anti-cancer drug and Cu/Zn-doped boron nitride nanocages as a drug delivery

Targeted drug delivery along with the most negligible side effects, is the most important challenge in the designing of the novel anti-cancer drug delivery. Therefore, the interaction of Cu/Zn-doped boron nitride nanocages as the carrier for Mercaptopurine (MP) anti-cancer drug was studied by density functional theory calculations to design a novel carrier. The adsorption of MP drug on Cu/Zn-doped boron nitride nanocages is suitable energetically. In this study, electronic parameters and Gibbs free energy of complexes of Cu/Zn-doped boron nitride nanocages with two configuration MP drug (N and S) were investigated. In addition, CuBN has a short recovery time, but ZnBN has more selectivity for MP drug. It is predicted that the MP drug over both Cu/Zn-doped boron nitride nanocages can be used as a suitable drug delivery system. Configuration -S of MP drug in both nanocage is more appropriate than configuration -N. Analysis of frontier molecular orbitals, UV-VIS spectra and density of states plots of the designed complexes confirmed adsorption MP drug on Cu/Zn-doped boron nitride nanocages. This research predicted which Cu/Zn-doped boron nitride nanocages can be used as acceptable carriers for MP anti-cancer drug.Communicated by Ramaswamy H. Sarma.

Electronic Effects in Phosphino-Iminophosphorane PdII Complexes upon Varying the N Substituent

Three series of palladium(II) complexes supported by a phosphine-iminophosphorane ligand built upon an ortho-phenylene core were investigated to study the influence of the iminophosphorane N substituent. Cis-dichloride palladium(II) complexes 1 in which the N atom bears an isopropyl (iPr, 1 a), a phenyl (Ph, 1 b), a trimethylsilyl (TMS, 1 c) group or an H atom (1 d) were synthesized in high yield. They were characterized by NMR, IR spectroscopy, HR-mass spectrometry, elemental analysis, and X-ray diffraction. A substantial bond length difference between the Pd-Cl bonds was observed in 1. Complexes 1 a-d were converted into [Pd(LR )Cl(CNt Bu)](OTf)] 2 a-d whose isocyanide is located trans to the iminophosphorane. The corresponding dicationic complexes [Pd(LR )(CNt Bu)2 ](OTf)2 3 a-d were also synthesized, however they exhibited lower stability in solution than 2, the isopropyl derivative 3 a being the most stable of the series. Molecular modeling was performed to rationalize the regioselectivity of the substitution of the single chloride by isocyanide (from 1 to 2) and to study the electronic distribution in the complexes. In particular differences between the TMS and H containing complexes vs. the iPr and Ph ones were found. This suggests that the nature of the N substituent is far from innocent and can help tune the reactivity of iminophosphorane complexes.

Design, Transport/Molecular Scale Electronics, Electric Properties, and a Conventional Quantum Study of a New Potential Molecular Switch for Nanoelectronic Devices

In this study, we examined the influence of an external electric field applied in two directions: horizontal (X-axis) and vertical (Y-axis) on the electronic and vibrational properties of a field-effect molecular switch, denoted as M. We employed density functional theory and quantum theory of atoms in molecules for this analysis. The current-voltage (I-V) characteristic curve of molecular switch system M was computed by applying the Landauer formula. The results showed that the switching mechanism depends on the direction of the electric field. When the electric field is applied along the X-axis and its intensity is around 0.01 au, OFF/ON switching mechanisms occur. By utilizing electronic localization functions and localized-orbital locator topological analysis, we observed significant intramolecular electronic charge transfer "back and forth" in Au-M-Au systems when compared to the isolated system. The noncovalent interaction revealed that the Au-M-Au complex is also stabilized by electrostatic interactions. However, if the electric field is applied along the Y-axis, a switching mechanism (OFF/ON) occurs when the electric field intensity reaches 0.008 au. Additionally, the local electronic phenomenological coefficients (Lelec) of this field-effect molecular switch were determined by using the Onsager phenomenological approach. It can also be predicted that the molecular electrical conductance (G) increases as Lelec increases. Finally, the electronic and vibrational properties of the proposed models M and Au-M-Au exhibit a powerful switching mechanism that may potentially be employed in a new generation of electronic devices.

Utilizing coordination chemistry through formation of a CuII-quinalizarin complex to manipulate cell biology: An in vitro, in silico approach

Quinalizarin, an analogue of anthracycline anticancer agents, is an anticancer agent itself. A CuII complex was prepared and characterized by elemental analysis, UV-Vis & IR spectroscopy, mass spectrometry, EPR and DFT. The intention behind the preparation of the complex was to increase cellular uptake, compare its binding with DNA against that of quinalizarin, modulation of semiquinone formation, realization of human DNA topoisomerase I & human DNA topoisomerase II inhibition and observation of anticancer activity. While the first two attributes of complex formation lead to increased efficacy, decrease in semiquinone generation could results in a compromise with efficacy. Inhibition of human DNA topoisomerase makes up this envisaged compromise in free radical activity since the complex shows remarkable ability to disrupt activities of human DNA topoisomerase I and II. The complex unlike quinalizarin, does not catalyze flow of electrons from NADH to O2 to the extent known for quinalizarin. Hence, decrease in semiquinone or superoxide radical anion could make modified quinalizarin [as CuII complex] less efficient in free radical pathway. However, it would be less cardiotoxic and that would be advantageous to qualify it as a better anticancer agent. Although binding to calf thymus DNA was comparable to quinalizarin, it was weaker than anthracyclines. Low cost of quinalizarin could justify consideration as a substitute for anthracyclines but the study revealed IC50 of quinalizarin/CuII-quinalizarin was much higher than anthracyclines or their complexes. Even then, there is a possibility that CuII-quinalizarin could be an improved and less costly form of quinalizarin as anticancer agent.

Metallo-dithiaporphyrin pigments for bulk-heterojunction solar cell applications: ab initio investigation of structural and optoelectronic properties

Metallo-dithiaporphyrin small molecules have been designed by substituting Ru(ii) with various transition metals at the same oxidation state (M = Mn, Fe, Ni, Cu) as donor materials for Bulk Heterojunction Organic Solar Cells (BHJ-OSCs). Density functional theory (DFT) and time-dependent DFT (TD-DFT) have been used to study the optoelectronic properties of metallo-dithiaporphyrin at various functionals and basis sets. We discovered that the open-circuit voltage (VOC) value increases when Ru(ii) in Ru(S2TTP)Cl2 (S2TTP = tetra-p-tolyldithiaporphyrin) is substituted. In addition, the light harvesting efficiency (LHE) of nickel, manganese, and iron complexes was found to be similar to that of ruthenium, and the iron complex furthermore presented a comparable charge transfer in the excited state corresponding to the Q-band, compared to Ru(S2TTP)Cl2. Hence M(S2TTP)Cl2 (M = Mn, Fe, Ni) appear to be potential low cost candidate donor molecules within a bulk heterojunction solar cell. We further propose suitable engineered acceptor pigments, fitted to provide a good overall solar cell efficiency.

Imidazolium-Based Ionic Liquid-Assisted Silver Nanoparticles and Their Antibacterial Activity: Experimental and Density Functional Theory Studies

The exclusive properties of ionic liquids (ILs) offer various opportunities to develop advanced materials with appreciable therapeutic applications. Imidazolium-based ILs have been frequently used as reaction media and stabilizers for the development and surface functionalization of noble metal nanoparticles (NPs). This study reports the citrate-mediated reduction of silver ions in three different ILs, that is, 1-ethyl-3-methylimidazolium methyl sulfate ([EMIM][MS]), 1-butyl-3-methylimidazolium trifluoromethanesulfonate ([BMIM][OTf]), and 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([BMIM][TFSI]). The resulting Ag-ILs NPs were characterized using many analytical techniques, including UV-visible spectroscopy, dynamic light scattering (DLS), scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction (XRD). DLS and XRD characterization revealed the negatively charged Ag-[EMIM][MS] NPs, Ag-[BMIM][OTf] NPs, and Ag-[BMIM][TFSI] NPs with mean hydrodynamic sizes of 278, 316, and 279 nm, respectively, and a face-centered cubic structure. These hybrid nanomaterials were subjected to in vitro antibacterial screening against three bacterial strains. The Ag-[BMIM][OTf] NPs exhibited significant activities against Escherichia coli, Staphylococcus aureus, and Enterobacter cloacae. The lowest inhibition concentration of 62.5 μg/mL was recorded against E. coli using Ag-[EMIM][MS] and Ag-[BMIM][OTf] NPs. Further, the density functional theory calculations carried out on the computed Ag-ILs in the gas phase and water showed relatively stable systems. Ag-[BMIM][TFSI] exhibited the lowest Gibbs free energy change of -34.41 kcal/mol. The value of the global electrophilicity index (ω = 0.1865 eV) for the Ag-[BMIM][OTf] correlated with its good antibacterial activity.

Encapsulation of heavy metal ions via adsorption using cellulose/ZnO composite: First principles approach

The primary goal of the current research is to describe an effective and eco-friendly adsorbent for the removal of aquatic micropollutants. The design of the cellulose-modified zinc oxide (ZnO) nanocomposite was successfully carried out by density functional calculations. The proposed structures of the constituent and composite materials were confirmed using formation energy (Ef), frontier orbitals, band gaps (Egap), density of state (DOS) plots, natural bond orbitals (NBO), and UV-Vis spectral analysis. The cellulose/(ZnO)12 composite was further used for the adsorption of different heavy metal ions such as Hg(II), Pb(II), Cd(II), Ni(II), and As(III) through calculation of electronic and optical properties. The values of the adsorption energy (Eads) show that the As(III) interacted better with the composite in both phases, i.e., gas (-806.98 kcal/mol) and aqueous (-491.66 kcal/mol). The analysis of frontier molecular orbital data exhibited a decrease in the Egap of composite@metal ion complexes. The high negative value of the solvation energies (ΔEsol) indicates the suitability of composite@metal ions in an aqueous environment. The nature of interactions between metal ions and the composite unit is analyzed by noncovalent interactions (NCI) and the quantum theory of atoms in molecules (QTAIM). The theoretical results of the present study show the feasibility of the cellulose/(ZnO)12 composite for the removal of heavy metal ions and provide useful information to experimentalists to treat contaminated water.

Ab Initio investigation for DNA nucleotide bases sequencing using chiral carbon nanobelts and nanotubes

Understanding the interaction mechanism between DNA nucleotide bases and carbon nanomaterials is an important issue in the field of identifying nucleotide molecules sequencing. In this article, the adsorption behavior of DNA nucleotide bases on the external surface of chiral carbon nanobelts (CNBs) (6, 5), (7, 6) and (8, 6), was comprehensively investigated from electronic and optical perspectives. As a result, it was determined that the DNA nucleotide bases have optical absorption in the ultraviolet region. When bases are adsorbed on the surface of CNBs, the optical absorption peak of the new complex structure shifted to the visible region. The study of the optical properties of selected CNBs showed that CNB (6,5) performs better in detecting Cytosine and the red shift in the absorption spectrum of complex structure is noticeable. Also, the effect of infinite length for chiral CNTs in DNA nucleotide base sequencing was investigated using DFTB approach. Our investigations based on electronic properties showed that CNTs have better performance than CNBs in DNA nucleotide base sequencing.

Coordinating Etching Inspired Synthesis of Fe(OH)3 Nanocages as Mimetic Peroxidase for Fluorescent and Colorimetric Self-Tuning Detection of Ochratoxin A

The development of multifunctional biomimetic nanozymes with high catalytic activity and sensitive response is rapidly advancing. The hollow nanostructures, including metal hydroxides, metal-organic frameworks, and metallic oxides, possess excellent loading capacity and a high surface area-to-mass ratio. This characteristic allows for the exposure of more active sites and reaction channels, resulting in enhanced catalytic activity of nanozymes. In this work, based on the coordinating etching principle, a facile template-assisted strategy for synthesizing Fe(OH)₃ nanocages by using Cu₂O nanocubes as the precursors was proposed. The unique three-dimensional structure of Fe(OH)₃ nanocages endows it with excellent catalytic activity. Herein, in the light of Fe(OH)₃-induced biomimetic nanozyme catalyzed reactions, a self-tuning dual-mode fluorescence and colorimetric immunoassay was successfully constructed for ochratoxin A (OTA) detection. For the colorimetric signal, 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) can be oxidized by Fe(OH)₃ nanocages to form a color response that can be preliminarily identified by the human eye. For the fluorescence signal, the fluorescence intensity of 4-chloro-1-naphthol (4-CN) can be quantitatively quenched by the valence transition of Ferric ion in Fe(OH)₃ nanocages. Due to the significant self-calibration, the performance of the self-tuning strategy for OTA detection was substantially enhanced. Under the optimized conditions, the developed dual-mode platform accomplishes a wide range of 1 ng/L to 5 μg/L with a detection limit of 0.68 ng/L (S/N = 3). This work not only develops a facile strategy for the synthesis of highly active peroxidase-like nanozyme but also achieves promising sensing platform for OTA detection in actual samples.

An insight into the mixed quantum mechanical-molecular dynamic simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations

An important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with Zn^II, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule of water bound to Zn^II. It arrests degradation of HCur to a considerable extent that was realized by taking it in phosphate buffer and in biological milieu. The structure was obtained by DFT calculations. Stable adduct formation was identified between optimized structures of HCur and [Zn(Cur)] with DNA (PDB ID: 1BNA) through experiments validated with multiscale modeling approach. Molecular docking studies provide 2D and 3D representations of binding of HCur and [Zn(Cur)] through different non-covalent interactions with the nucleotides of the chosen DNA. Through molecular dynamics simulation, a detailed understanding of binding pattern and key structural characteristics of the generated DNA-complex was obtained following analysis by RMSD, RMSF, radius of gyration, SASA and aspects like formation of hydrogen bonds. Experimental studies provide binding constants for [Zn(Cur)] with calf thymus DNA at 25 °C that effectively helps one to realize its high affinity towards DNA. In the absence of an experimental binding study of HCur with DNA, owing to its tendency to degrade in solution, a theoretical analysis of the binding of HCur to DNA is extremely helpful. Besides, both experimental and simulated binding of [Zn(Cur)] to DNA may be considered as a case of pseudo-binding of HCur to DNA. In a way, such studies on interaction with DNA helps one to identify HCur's affinity for cellular target DNA, not realized through experiments. The entire investigation is an understanding of experimental and theoretical approaches that has been compared continuously, being particularly useful when a molecule's interaction with a biological target cannot realized experimentally.

What Other Than Acridinium Esters? Computational Search for New Acridinium-Based Chemiluminogens

The rapid increase in disease prevalence in the world makes it extremely important to search for new or develop existing diagnostic methods, for example, chemiluminescent labeling used in immunodiagnostics. At present, acridinium esters are willingly used as chemiluminogenic fragments of labels. However, the search for new chemiluminogens that are particularly efficient is the main task of our studies. The density functional theory (DFT) and time-dependent (TD) DFT methods were used to obtain thermodynamic and kinetic results concerning the chemiluminescence and competitive dark reactions, which indicated whether some of the scrutinized derivatives have better characteristics than the chemiluminogens used so far. Synthesis of these candidates for efficient chemiluminogens, followed by studies of their chemiluminescent properties, and ultimately in chemiluminescent labeling, are further steps to confirm their potential applicability in immunodiagnostics.

Properties of Naked Silver Clusters with Up to 100 Atoms as Found with Embedded-Atom and Density-Functional Calculations

The structural and energetic properties of small silver clusters Agn with n = 2-100 atoms are reported. For n = 2-100 the embedded atom model for the calculation of the total energy of a given structure in combination with the basin-hopping search strategy for an unbiased structure optimization has been used to identify the energies and structures of the three energetically lowest-lying isomers. These optimized structures for n = 2-11 were subsequently studied further through density-functional-theory calculations. These calculations provide additional information on the electronic properties of the clusters that is lacking in the embedded-atom calculations. Thereby, also quantities related to the catalytic performance of the clusters are studied. The calculated properties in comparison to other available theoretical and experimental data show a good agreement. Previously unidentified magic (i.e., particularly stable) clusters have been found for n>80. In order to obtain a more detailed understanding of the structural properties of the clusters, various descriptors are used. Thereby, the silver clusters are compared to other noble metals and show some similarities to both copper and nickel systems, and also growth patterns have been identified. All vibrational frequencies of all the clusters have been calculated for the first time, and here we focus on the highest and lowest frequencies. Structural effects on the calculated frequencies were considered.

Mechanistic Investigation of the Synthesis of Dianionic In-Derived Coordination Polymers

The mechanism of formation of crystalline coordination polymers is as complex as the architectures themselves. In this Communication, we detail a three-tiered approach using density functional theory (DFT) analysis, synthesis, and in situ Raman spectroscopy to study the formation of coordination polymers. Specifically, the previously reported coordination polymers YCM-22 and YCM-51 containing the [In(CO₂R)₂X₃]^2- (X = halogen) molecular building unit (MBU) were investigated. DFT revealed two potential pathways of formation, involving the initial formation of either [InCl₄]^- or [In(CO₂R)Cl₃]^-. A molecular dimeric In species (8a) containing two [In(CO₂R)Cl₄]^2- centers bridged by 2,5-thiophenedicarboxylic acid was isolated. When a suspension of 8a was treated with a solution of 2,5-thiophenedicarboxylic acid, an isomer of the coordination polymer YCM-22 (denoted as YCM-22') was formed. In situ Raman analysis of the formation of YCM-22 confirms that [InCl₄]^- forms at the onset of the reaction and that the [In(CO₂R)₂X₃]^2- MBU forms at its expense. The totality of the data presented support a mechanism of formation of one-dimensional In-derived coordination polymers and present a roadmap for future investigations into the formation of other crystalline coordination polymers.

Carbon nanotubes and nanobelts as potential materials for biosensor

We investigate the electronic response of single-walled carbon nanotubes (SWCNTs) and a carbon nanobelt (CNB) to N-linked and O-linked SARS-CoV-2 spike glycoproteins, using ab initio quantum mechanical approach. The CNTs are selected from three zigzag, armchair, and chiral groups. We examine the effect of carbon nanotube (CNT) chirality on the interaction between CNTs and glycoproteins. Results indicate that the chiral semiconductor CNTs clearly response to the presence of the glycoproteins by changing the electronic band gaps and electron density of states (DOS). Since the changes in the CNTs band gaps in the presence of N-linked are about two times larger than the changes in the presence of the O-linked glycoprotein, chiral CNT may distinguish different types of the glycoproteins. The same results are obtained from CNBs. Thereby, we predict CNBs and chiral CNTs have suitable potential in sequential analysis of N- and O-linked glycosylation of the spike protein.

Synthesis, Empirical and Theoretical Investigations on New Histaminium Bis(Trioxonitrate) Compound

In this paper, a novel hybrid material, entitled histaminium bis(trioxonitrate), with the general chemical formula (C₅H₁₁N₃)(NO₃)₂, denoted by HTN was presented. Single-crystal X-ray diffraction was used to determine the structural characteristics of this compound after it was made using a slow evaporation method at room temperature. This compound was elaborated and crystallized to the monoclinic system with space group P2₁/c, and the lattice parameters obtained were: a = 10.4807 (16)Å, b = 11.8747 (15)Å, c = 16.194 (2)Å, β = 95.095 (6)°, V = 2007.4 (5)ų and Z = 8. The title compound's atomic structure couldbe modeled as a three-dimensional network. Organic cations and nitrate anions were connected via N-H...O and C-H...O hydrogen bonds in the HTN structure. The intermolecular interactions responsible for the formation of crystal packing were evaluated using Hirshfeld surfaces and two-dimensional fingerprint plots. The compound's infrared spectrum, which ranged from 4000 to 400 cm^-1, confirmed the presence of the principal bands attributed to the internal modes of the organic cation and nitrate anions. Additionally, spectrofluorimetry and the ultraviolet-visible spectrum was used to investigate this compound. DFT calculations were used to evaluate the composition and properties of HTN. The energy gap, chemical reactivity and crystal stability of HTN were quantified by performing HOMO-LUMO frontier orbitals analysis. Topological analysis (AIM), Reduced Density Gradient (RDG), molecular electrostatic potential surface (MEPS) and Mulliken population were processed to determine the types of non-covalent interactions, atomic charges and molecular polarity in detail.

Discriminative 'Turn-on' Detection of Al3+ and Ga3+ Ions as Well as Aspartic Acid by Two Fluorescent Chemosensors

In this work, two Schiff-base-based chemosensors L1 and L2 containing electron-rich quinoline and anthracene rings were designed. L1 is AIEE active in a MeOH-H₂O solvent system while formed aggregates as confirmed by the DLS measurements and fluorescence lifetime studies. The chemosensor L1 was used for the sensitive, selective, and reversible 'turn-on' detection of Al³⁺ and Ga³⁺ ions as well as Aspartic Acid (Asp). Chemosensor L2, an isomer of L1, was able to selectively detect Ga³⁺ ion even in the presence of Al³⁺ ions and thus was able to discriminate between the two ions. The binding mode of chemosensors with analytes was substantiated through a combination of ¹H NMR spectra, mass spectra, and DFT studies. The 'turn-on' nature of fluorescence sensing by the two chemosensors enabled the development of colorimetric detection, filter-paper-based test strips, and polystyrene film-based detection techniques.

Lantern-type dinickel complexes: An exploration of possibilities for nickel-nickel bonding with bridging bidentate ligands

Many binuclear nickel complexes have NiNi distances suggesting NiNi covalent bonds, including lantern-type complexes with bridging bidentate ligands. This DFT study treats tetragonal, trigonal, and digonal lantern-type complexes with the formamidinate, guanidinate, and formate ligands, besides some others. Formal bond orders (ranging from zero to two) are assigned to all the NiNi bonds on the basis of MO occupancy considerations. A VB-based electron counting approach assigns plausible resonance structures to the dinickel cores. Model tetragonal complexes with the dimethylformamidinate and the dithioformate ligands have singlet ground states whose non-covalently bonded NiNi distances are close to those in their experimentally known counterparts. Trigonal dinickel complexes are unknown, but are predicted to have quartet ground states with NiNi bonds of order 0.5. The model digonal complexes are predicted to have triplet ground states, but the predicted NiNi bond lengths are longer than those found in their experimentally known counterparts. This could owe to inadequate treatment of electron correlation by DFT in these short NiNi bonds with their multiconfigurational character. All the NiNi bond distances here are categorized into ranges according to the NiNi bond orders of 0, 0.5, 1, 1.5, and 2, no NiNi bonds of order higher than two being identified. The NiNi bonds of given order in these lantern-type complexes are consistently shorter than the corresponding NiNi bonds in dinickel complexes having carbonyl ligands, attributable to the metalmetal bond lengthening effect of CO ligands.

Atroposelective Synthesis of Triaryl α-Pyranones with 1,2-Diaxes by N-Heterocyclic Carbene Organocatalysis

Atropisomers bearing multiple stereogenic axes are of increasing importance to the field of material science, pharmaceuticals, and catalysis. However, the atroposelective construction of multi-axis atropisomers remains rare and challenging, due to the intrinsical difficulties in the stereo-control of the multiple stereogenic axes. Herein, we demonstrate a single-step construction of a new class of 1,2-diaxially chiral triaryl α-pyranones by an N-heterocyclic carbene organocatalytic asymmetric [3+3] annulation of well-designed alkynyl acylazolium precursors and enolizable sterically hindered 2-aryl ketones. The protocol features broad substrate scope (>50 examples), excellent stereo-control (most cases >20 : 1 dr, up to 99.5 : 0.5 er), and potentially useful synthetic applications. The success of this reaction relies on the rational design of structurally matched reaction partners and the careful selection of the asymmetric catalytic system. DFT calculations have also been performed to discover and rationalize the origin of the high stereoselectivity of this reaction.

Photodegradation of dye using Polythiophene/ZnO nanocomposite: A computational approach

Incorporating nanostructured photocatalysts in polymers is a strategic way to obtain novel water purification systems. Here, we present density functional theory (DFT) study of Polythiophene/Zinc oxide (PTh/ZnO) nanocomposite with high photocatalytic performance and stability which exhibits superior degradation of alizarine dye under the visible light condition with interaction energy of -149.55 kcal/mol between conducting polymer (PTh) and metal oxide, with PTh sponsoring more number of electrons to the conduction band of ZnO. The electrical and optical properties of optimized geometries of PTh/ZnO nanocomposite were studied by frontier molecular orbital analysis, natural bond orbital (NBO) charge simulation, natural electronic configuration, and UV-vis absorption spectra. The modulation of the energy band gap (∽ 2.60 eV) and exciton binding energy (∽ 0.36 eV) causes visible light absorption and hence enhances the photodegradation activity of PTh/ZnO. NBO analysis evidences the electron accepting behavior of ZnO in the composites as it withdraws electron cloud density of about 0.14e from the polymer unit.

Adsorption properties of metal functionalized fullerene (C59Au, C59Hf, C59Ag, and C59Ir) nanoclusters for application as a biosensor for hydroxyurea (HXU): insight from theoretical computation

This theoretical study was conducted to evaluate the efficiency of fullerene C60 and its metal functionalized nano clusters (C59Au, C59Hf, C59Ag and C59Ir) as a sensor for hydroxyurea (HXU). The various conclusions concerning the adsorption and sensing properties of the studied nano surfaces were achieved using density functional theory (DFT) at the M062X-D3/gen/LanL2DZ/def2svp level of theory. Among the nano clusters studied for this interaction, analysis of the HOMO–LUMO energy differences (E g) showed that HXU@C59Hg (H2) reflects the least energy gap of 3.042 eV, indicating its greater reactivity, sensitivity and conductivity. Also, the adsorption phenomenon in this current study is best described as chemisorptions owing to the negative adsorption enthalpies observed. Thus, the adsorption energy (E Ad) follows an increasing pattern of: HXU@C60 (C1) (−0.218 eV) < HXU@C59Ir (I1) (−1.361 eV) < HXU@C59Au (A1) (−1.986 eV) < HXU@C59Hf (H1) (−2.640 eV) < HXU@C59Hg (H2) (−3.347 eV). Least E g, highest E Ad and non-covalent nature of interaction attributed to C59Hg surface are sufficient to show that, among all studied surfaces, C59Hg surface emerged as the most suitable adsorbent for the adsorption of HXU. Hence, it can be used in modeling future adsorbent material for hydroxyurea.

Quantum chemical hydrogenolysis strategy for elimination of heteroatoms in biomass homologous organic compounds based on oxolane and thiolane

Bio-oils obtained from biomass contain heteroatoms compounds, like oxolane and thiolane. It is quite difficult for industrialist to purify such refractory bio-oils. One of the efficient strategies for the elimination of heteroatoms is hydrogenolysis process, which results in the formation of H₂O and H₂S residues as by-products. In this work, quantum chemical studies have been used to analyse the reaction mechanism for the removal of hetero atoms (S and O) as H₂O and H₂S. We selected B3LYP functional of DFT with Pople's basis set 6-311G(d,p) for computing the hydrogenolysis steps without catalyst. LANL2DZ basis set, is used for studying hydrogenolysis steps involving AlCl₃ and WS₃H₃⁺ as catalysts. All the reactions are analysed at the temperature of 600 K and pressure of 40 bars. Structural, thermodynamic, kinetic properties have been employed to study this process. The analysis of variations parameters during the hydrogenolysis process reveals that these two organic biomass compounds undergo sequential ring opening at C-X (X = O, S) bonds. Butanol and Butanethiol are obtained as a result of first hydrogenolysis process, and these compounds are converted to butane during second catalytic process while eliminating heteroatoms.

Basically, nucleophilicity matters little: towards unravelling the supramolecular driving forces in enzyme-like CO2 conversion

The reaction mechanism for the cycloaddition of CO₂ to styrene oxide in the presence of macrocyclic pseudopeptides has been studied using DFT methods. Computational calculations indicate that the unprecedented catalytic behaviour previously observed experimentally, in which the most reactive species was not the most nucleophilic but the most basic one, can be associated to the tight cooperativity between several supramolecular interactions promoted by simple peptidomimetics able to display a synzymatic behaviour. This bizarre catalytic performance afforded remarkable conversions of a sluggish substrate like styrene oxide into the desired cyclic carbonate, even under relatively mild reaction conditions, opening the way for the practical use of CO₂ as a raw material in the preparation of valuable chemicals. Furthermore, the remote modification of essential structural features of the macrocycle (synzyme engineering) permitted the driving forces of the synzymatic system to be analyzed, stressing the crucial synergic effect between an elegantly preorganized oxyanion hole and additional aromatic interactions.

New Organic-Inorganic Salt Based on Fluconazole Drug: TD-DFT Benchmark and Computational Insights into Halogen Substitution

In this study, we report the synthesis of a new organic–inorganic molecular salt of the clinically used antifungal drug fluconazole, (H2Fluconazole).SnCl₆.2H₂O. By detailed investigation and analysis of its structural properties, we show that the structure represents a 0D structure built of alternating organic and inorganic zig-zag layers along the crystallographic c-axis and the primary supramolecular synthons in this salt are hydrogen bonding, F···π and halogen bonding interactions. Magnetic measurements reveal the co-existence of weak ferromagnetic behavior at low magnetic field and large diamagnetic contributions, indicating that the synthesized material behaves mainly as a diamagnetic material, with very low magnetic susceptibility and with a band gap energy of 3.6 eV, and the salt is suitable for semiconducting applications. Extensive theoretical study is performed to explain the acceptor donor reactivity of this compound and to predict the Cl-substitution effect by F, Br and I. The energy gap, frontier molecular orbitals (FMOs) and the different chemical reactivity descriptors were evaluated at a high theoretical level. Calculations show that Cl substitution by Br and I generates compounds with more important antioxidant ability and the intramolecular charge transfer linked to the inorganic anion.

Efficient model photosensitizers based on metallocenyl complexes with thiophene-N = N-pyrimidine as π-conjugated bridge and cyanoacrylate as an anchoring group: a density functional theory study

Eight push-pull systems involving containing four transition metals (iron, ruthenium, cobalt, and nickel), metallocenes as donor groups, cyanoacrylate as electron attractor group, and thiophene-N = N- pyrimidine derivatives as π-conjugated bridges were designed and studied using DFT and TD-DFT methods involving B3LYP and CAM-B3LYP functionals combined with the cc-pVDZ/LANL2DZ basis sets. The main purpose of this work is to determine the effect of metallocene in improving the photosensitization property of such chromophores. This was done by calculating their light-harvesting efficiency LHE as well as other properties employed for DSSC application. The considered dyes were first studied in the gas phase, then in the presence of TiO₂ nanoparticles representing the semi-conductor, and finally in the presence of a specific implicit solvent. The presence of iron as metal involved in the metallocene group supplemented by extending the π-conjugated bridge by a cyanovinyl spacer was demonstrated so as to give the most optimal response taking into account the lower cost and toxicity as well as the friendliness to the environment of iron as metal.

A detailed theoretical investigation to unravel the molecular mechanism of the ligand-free copper-catalyzed Suzuki cross-coupling reaction

The Suzuki-Miyaura coupling (SMC) represents a very efficacious method for constructing C-C bonds in organic synthesis. The ligand-free variants of SMC have been grabbing attention these days. Despite this momentousness, the mechanistic details of the ligand-free variants are scant in the literature. Herein, we have carried out a detailed mechanistic investigation into the ligand-free Cu-catalyzed SMC of unsaturated organic halides with aryl boronic acid with the aid of density functional theory (DFT) calculations employing the conductor-like polarizable continuum model (CPCM) method. The present study elucidates that in the absence of ancillary ligands on the metal, the substrates, base, and solvent molecules could act as pseudo-ancillary ligands to facilitate the cross-coupling reaction. The investigation further revealed that unsaturated halides like alkynyl halides/vinyl halides could act as good ancillary ligands for copper by forming a Cu-π intermediate and promoting a facile transmetalation process. However, regarding the oxidative addition and reductive elimination steps, a concerted pathway is observed contrary to Pd catalyzed Suzuki coupling, owing to the instability of Cu(III) species and the favourability of Csp²-Csp bond formation. In the whole set of mechanisms explored, oxidative addition/oxidative nucleophilic substitution was the rate-determining step in all the cases. A thermodynamically stable π-coordinated intermediate species where the substrate and base molecule are coordinated to the metal center is identified as the rate-determining species for the ligand-free Suzuki cross-coupling reaction. The presence of the aforesaid intermediate increases the energy span and consequently the activation barrier for the rate-determining step. This study unveiled a theoretical rationale for the high-temperature requirement in the ligand-free Cu-catalyzed SMC reaction.