Structure Of Complex Research Articles

Formation of Inclusion Complexes of 2-Hydroxypropyl β-Cyclodextrin with 2-Hydroxychalcone: Experimental and Theoretical Study

The formation of inclusion complexes of 2-hydroxypropyl-β-cyclodextrin (HP β-CD) with 2-hydroxychalcone (2HOCH) in solution and solid state was investigated using UV–Visible, fluorescence, Fourier transform-infrared (FT-IR) spectroscopy, powder X-ray diffraction (PXRD), scanning electron microscope (SEM) techniques. The results obtained confirmed that 2HOCH formed the stable inclusion complex with HP β-CD. Moreover, the spectral data and Benesi–Hildebrand plots results indicated that the stoichiometry of the inclusion complex was 1:1. Theoretically, the structure of the inclusion complexes and the physical parameters such as complexation energy, highest occupied molecular orbital–lowest unoccupied molecular orbital, and energy gap were obtained using the DFT/B3LYP/6-311G method. It was found that the complexation energy for orientation B was lower than that for orientation A as evidenced by the theoretical calculations. Moreover, the carbonyl group of molecules was located outside of the cyclodextrin cavity while the hydroxyl group was located inside the cavity. The antioxidant capacity and antibacterial responses of the inclusion complexes and, for comparison, the parent compounds were also carried out.

MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes.

The lysosomal degradation of macromolecules produces diverse small metabolites exported by specific transporters for reuse in biosynthetic pathways. Here we deorphanized the major facilitator superfamily domain containing 1 (MFSD1) protein, which forms a tight complex with the glycosylated lysosomal membrane protein (GLMP) in the lysosomal membrane. Untargeted metabolomics analysis of MFSD1-deficient mouse lysosomes revealed an increase in cationic dipeptides. Purified MFSD1 selectively bound diverse dipeptides, while electrophysiological, isotope tracer and fluorescence-based studies in Xenopus oocytes and proteoliposomes showed that MFSD1-GLMP acts as a uniporter for cationic, neutral and anionic dipeptides. Cryoelectron microscopy structure of the dipeptide-bound MFSD1-GLMP complex in outward-open conformation characterized the heterodimer interface and, in combination with molecular dynamics simulations, provided a structural basis for its selectivity towards diverse dipeptides. Together, our data identify MFSD1 as a general lysosomal dipeptide uniporter, providing an alternative route to recycle lysosomal proteolysis products when lysosomal amino acid exporters are overloaded.

Spectrophotometric determination of cobalt ions in water using bimetallic chemosensor based on sulfa drug azo dye

AbstractA spectrophotometric technique has been developed for detection of cobalt(II) ions in aqueous solution samples utilising a new chemosensor. This technique relies on the formation of a stable yellow-orange complex at pH = 13 using 4-(2-Hydroxy-naphthalen-1-ylazo)-N-thiazol-2-yl-benzenesulfonamide (H2L) as ligand through complexation with Co(II) ions. At λ = 390 nm, complex absorption was detected. A correlation coefficient of 0.9934 indicated linearity in the concentration range of (1.7–8.4 × 10–5 mol L−1). The limit of detection (LOD) and limit of quantification (LOQ) were assigned to be 0.147 µg ml−1 (2.5 µmol L−1) and 0.489 µg ml−1 (8.3 µmol L−1),respectively. The stoichiometric composition of the complex, which is 2:1 of M:L, was confirmed by the correlation between the continuous variation results and the molar-ratio methods proposed by Job. Additionally, the structure of the solid complex that is produced when H2L reacts with Co(NO3)2.6H2O has been determined by applying different spectroscopic and analytical techniques, confirming the formation of the complex in the same molar ratio as that determined by Job’s method. The geometrical structure of the complex was confirmed to be tetrahedral by a combination of magnetic moment results and UV-Vis spectra.

Inhibition mechanisms of CRISPR-Cas9 by AcrIIA25.1 and AcrIIA32.

In the ongoing arms race between bacteria and bacteriophages, bacteriophages have evolved anti-CRISPR proteins to counteract bacterial CRISPR-Cas systems. Recently, AcrIIA25.1 and AcrIIA32 have been found to effectively inhibit the activity of SpyCas9 both in bacterial and human cells. However, their molecular mechanisms remain elusive. Here, we report the cryo-electron microscopy structures of ternary complexes formed by AcrIIA25.1 and AcrIIA32 bound to SpyCas9-sgRNA. Using structural analysis and biochemical experiments, we revealed that AcrIIA25.1 and AcrIIA32 recognize a novel, previously-unidentified anti-CRISPR binding site on SpyCas9. We found that both AcrIIA25.1 and AcrIIA32 directly interact with the WED domain, where they spatially obstruct conformational changes of the WED and PI domains, thereby inhibiting SpyCas9 from recognizing protospacer adjacent motif (PAM) and unwinding double-stranded DNA. In addition, they may inhibit nuclease activity by blocking the dynamic conformational changes of the SpyCas9 surveillance complex. In summary, our data elucidate the inhibition mechanisms of two new anti-CRISPR proteins, provide new strategies for the modulation of SpyCas9 activity, and expand our understanding of the diversity of anti-CRISPR protein inhibition mechanisms.

Control Over Anion Coordination on Pd(II), Cu(I), and Ag(I) with Regioisomeric Phosphine-Carboxylate Ligands.

The coordination of anionic donors is involved at various stages of catalytic cycles in transition-metal catalysis, but control over the spatial positioning of anions around a metal center is a challenge in coordination chemistry. Here we show that regioisomeric phosphine-carboxylate ligands provide spatial anion control on palladium(II) centers by favoring either κ2, cis-κ1, or trans-κ1 coordination of the carboxylate donor. Additionally, the palladium(II) carboxylates, which contain a methyl donor, upon protonation, deliver metal-alkyl complexes that feature a coordinated carboxylic acid. Such complexes can be considered as models for the minima that follow the concerted metalation-deprotonation transition state for C-H activation. The predictability of the coordination modes is further demonstrated on silver(I) and copper(I) centers, for which less common structures of mononuclear and dinuclear complexes can be obtained by using spatial anion control. Our results demonstrate the potential for spatial control over carboxylate anions in coordination chemistry.

Copper-Based Complexes with Adamantane Ring-Conjugated bis(3,5-Dimethyl-pyrazol-1-yl)acetate Ligand as Promising Agents for the Treatment of Glioblastoma.

The new ligand L2Ad, obtained by conjugating the bifunctional species bis(3,5-dimethylpyrazol-1-yl)-acetate and the drug amantadine, was used as a chelator for the synthesis of new Cu complexes 1-5. Their structures were investigated by synchrotron radiation-induced X-ray photoelectron spectroscopy (SR-XPS), near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and by combining X-ray absorption fine structure (XAFS) spectroscopy techniques and DFT modeling. The structure of complex 3 was determined by single-crystal X-ray diffraction analysis. Tested on U87, T98, and U251 glioma cells, Cu(II) complex 3 and Cu(I) complex 5 decreased cell viability with IC50 values significantly lower than cisplatin, affecting cell growth, proliferation, and death. Their effects were prevented by treatment with the Cu chelator tetrathiomolybdate, suggesting the involvement of copper in their cytotoxic activity. Both complexes were able to increase ROS production, leading to DNA damage and death. Interestingly, nontoxic doses of 3 or 5 enhanced the chemosensitivity to Temozolomide.

The Importance of Structured Water in HDAC8 for Correct Binding Pose Applied for Drug Design of Anticancer Molecules.

Validating the docking procedure and maintaining the structural water molecules at HDAC8 catalytic site. Molecular docking simulations play a significant role in Computer-Aided Drug Design, contributing to the development of new molecules. To ensure the reliability of these simulations, a validation process called "Re-docking" is employed, focusing on the binding mode of a ligand co-crystallized with the protein of interest. In this study, several molecular docking studies were conducted using five X-ray structures of HDAC8-ligand complexes from the PDB. Ligands initially complexed with HDAC8 were removed and re-docked onto the free protein, revealing a poor reproduction of the expected binding mode. In response to this, we observed that most HDAC8-ligand complexes contained one to two water molecules in the catalytic site, which were crucial for maintaining the cocrystallized ligand. These water molecules enhance the binding mode of the co-crystallized ligand by stabilizing the proteinligand complex through hydrogen bond interactions between ligand and water molecules. Notably, these interactions are lost if water molecules are removed, as is often done in classical docking methodologies. Considering this, molecular docking simulations were repeated, both with and without one or two conserved water molecules near Zn+2 in the catalytic cavity. Simulations indicated that replicating the native binding pose of co-crystallized ligands on free HDAC8 without these water molecules was challenging, showing greater coordinate displacements (RMSD) compared to those including conserved water molecules from crystals. The study highlighted the importance of conserved water molecules within the active site, as their presence significantly influenced the successful reproduction of the ligands' native binding modes. The results suggest an optimal molecular docking procedure for validating methods suitable for filtering new HDAC8 inhibitors for future experimental assays.

Site-specific regulation of RNA editing with ribose-modified nucleoside analogs in ADAR guide strands.

Adenosine Deaminases Acting on RNA (ADARs) are enzymes that catalyze the conversion of adenosine to inosine in RNA duplexes. These enzymes can be harnessed to correct disease-causing G-to-A mutations in the transcriptome because inosine is translated as guanosine. Guide RNAs (gRNAs) can be used to direct the ADAR reaction to specific sites. Chemical modification of ADAR guide strands is required to facilitate delivery, increase metabolic stability, and increase the efficiency and selectivity of the editing reaction. Here,we show the ADAR reaction is highly sensitive to ribose modifications (e.g. 4'-C-methylation and Locked Nucleic Acid (LNA) substitution) at specific positions within the guide strand. Our studies were enabled by the synthesis of RNA containing a new, ribose-modified nucleoside analog (4'-C-methyladenosine). Importantly, the ADAR reaction is potently inhibited by LNA or 4'-C-methylation at different positions in the ADAR guide. While LNA at guide strand positions -1 and -2 block the ADAR reaction, 4'-C-methylation only inhibits at the -2 position. These effects are rationalized using high-resolution structures of ADAR-RNA complexes. This work sheds additional light on the mechanism of ADAR deamination and aids in the design of highly selective ADAR guide strands for therapeutic editing using chemically modified RNA.

Exploring the binding properties of DNA/BSA and cytotoxicity studies with new terpyridine-ester-based metal complexes (M = Fe(III), Ni(II), Cu(II) and Ru(III)) – A comparative analysis

Many terpyridines and their metal complexes are known to exhibit remarkable potential for the interaction of biological targets. Notably, a subtle change in the structure of the ligand can influence these interactions significantly. In this regard, it would be very interesting to assess the binding affinity of functionalized molecules with DNA/BSA. In this work, a novel ester-based terpyridine (L) and the corresponding four metal complexes with Ni(II) (MC1), Cu(II) (MC2), Fe(III) (MC3) and Ru(III) (MC4) were prepared and structurally characterized using various spectroscopic and analytical techniques including the validation of molecular structures of ligand (L) and Ni(II)-Tpy complex (MC1). The EPR data demonstrate that MC1 is diamagnetic and other complexes (MC2-MC4) exhibit paramagnetic behavior. Additionally, the structures of ligands and metal complexes were determined using DFT studies and the same were utilized for the docking studies. Interestingly, MC3 and MC4 exhibit a predominant lowest binding energy of −9.62 Kcal/mol (with DNA) and −10.05 Kcal/mol (with BSA) respectively. The binding affinity of the ligand and its complexes with protein and DNA was evaluated by spectroscopic techniques. Notably, the cytotoxicity studies of L and MC1-MC4 were performed against the MCF-7 (human breast cancer) cell lines. The complex MC4 displayed great activity with an IC50 of 3.5 ± 1.75 μM among all synthesized compounds and comparable with cisplatin.

Dinitrogen-bridged ruthenium(II) complexes featuring dithiocarbamate ligands

In quest of low molecular weight metal-thiolate complexes as model complexes for nitrogenase, four binuclear ruthenium(II) dinitrogen-bridged complexes featuring dithiocarbamate ligands, [{(Me3tacn)Ru(κ2-S2CNR2)}2(µ-N2)][PF6]2 (Me3tacn = 1,4,7-trimethyl-1,4,7-triazacyclononane; 1, R = Me; 2, R = Et; 3, R = nPr; 4, R = iPr), were synthesized by reduction of [(Me3tacn)RuIII(κ2-S2CNR2)Cl]PF6 with zinc powder in a nitrogen atmosphere. A 16-electron mononuclear ruthenium(II) species [(Me3tacn)Ru(κ2-S2CNnPr2)]PF6 (3′) was isolated during preparation of 3, which may help elucidate the formation of complexes 1-4. Molecular structures of complexes 1, 2, 4 and 3′ were established by single crystal X-ray diffraction analysis. Moreover, complexes 1-4 were characterized by infrared, 1H NMR, UV–vis, fluorescence, Raman (solid state and solution state) spectroscopies and mass spectrometry, and their electrochemical properties were also investigated. Density functional theory (DFT) calculation was performed on complex 2 to study its Lewis structure and explain the UV–vis absorption spectra. Structural and DFT analyses demonstrate that N2 activation is accompanied by electron redistribution of the dithiocarbamate ligands.

Cryo-EM structure and functional analysis of the chromatin remodeler RSF.

The RSF complex belongs to the ISWI chromatin-remodeling family and is composed of two subunits: RSF1 (remodeling and spacing factor 1) and SNF2h (sucrose nonfermenting protein 2 homolog). The RSF complex participates in nucleosome spacing and assembly, and subsequently promotes nucleosome maturation. Although SNF2h has been extensively studied in the last few years, the structural and functional properties of the remodeler RSF1 still remain vague. Here, a cryo-EM structure of the RSF-nucleosome complex is reported. The 3D model shows a two-lobe architecture of RSF, and the structure of the RSF-nucleosome (flanked with linker DNA) complex shows that the RSF complex moves the DNA away from the histone octamer surface at the DNA-entry point. Additionally, a nucleosome-sliding assay and a restriction-enzyme accessibility assay show that the RSF1 subunit may cause changes in the chromatin-remodeling properties of SNF2h. As a `nucleosome ruler', the results of an RSF-dinucleosome binding affinity test led to the proposal that the critical distance that RSF `measures' between two nucleosomes is about 24 base pairs.

Direct prediction of isotopic properties from molecular dynamics trajectories: Application to sulfide, sulfate and sulfur radical ions in hydrothermal fluids

In hydrothermal fluids, disulfur (S2•−) and trisulfur (S3•−) radical anions have been observed to coexist with the major hydrogen sulfide and sulfate species. These radical ions have potentially important effects on the solubility, transport and fractionation of metals and sulfur, with consequences for ore deposit formation and, more generally, for geochemical cycles of metals and volatiles. It is therefore essential to know the intrinsic isotopic properties of these important sulfur species in order to use sulfur isotopes for tracing different geological processes. Here, the theoretical equilibrium isotopic properties of the disulfur and trisulfur radical ions are computed and compared to the hydrogen sulfide (H2S) and sulfate ion (SO42−), using, for the first time, a first-principles molecular dynamics (MD) approach. The isotopic properties are calculated directly from molecular dynamics trajectories using the vibrational density of states and the atomic kinetic energy, and then compared to the more established method based on sampling of several snapshots. This comparison allowed us to validate the new modelling method and to assess its advantages and limitations. The predicted equilibrium isotope fractionation in terms of 34S/32S between S2•− and S3•− is small, i.e. <1‰, with a slight enrichment in the heavier isotope for S3•−, over the temperature range 200–500 °C. Both radical ions are slightly depleted in the heavier isotope, by 1 to 2‰, relative to aqueous H2S. Our results help tuning sulfur isotope fractionation models used for tracing the origin and evolution of hydrothermal fluids. Our method opens large perspectives for using the rapidly growing body of MD simulation data in geosciences on structure and stability of aqueous complexes to assess in parallel element isotope fractionations from MD-generated trajectories.

Benchmarking AlphaFold-Generated Structures of Chemokine-Chemokine Receptor Complexes.

AlphaFold and AlphaFold-Multimer have become two essential tools for the modeling of unknown structures of proteins and protein complexes. In this work, we extensively benchmarked the quality of chemokine-chemokine receptor structures generated by AlphaFold-Multimer against experimentally determined structures. Our analysis considered both the global quality of the model, as well as key structural features for chemokine recognition. To study the effects of template and multiple sequence alignment parameters on the results, a new prediction pipeline called LIT-AlphaFold (https://github.com/LIT-CCM-lab/LIT-AlphaFold) was developed, allowing extensive input customization. AlphaFold-Multimer correctly predicted differences in chemokine binding orientation and accurately reproduced the unique binding orientation of the CXCL12-ACKR3 complex. Further, the predictions of the full receptor N-terminus provided insights into a putative chemokine recognition site 0.5. The accuracy of chemokine N-terminus binding mode prediction varied between complexes, but the confidence score permitted the distinguishing of residues that were very likely well positioned. Finally, we generated a high-confidence model of the unsolved CXCL12-CXCR4 complex, which agreed with experimental mutagenesis and cross-linking data.

Linking Bulk and Surface Structures in Complex Mixed Oxides

Linking Bulk and Surface Structures in Complex Mixed Oxides

Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C.

The yeast SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a 'pincer-like' conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5-nucleosome complex suggests that promoter proximal, histone H2B ubiquitylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.

Structural and functional characterization of the role of acetylation on the interactions of the human Atg8-family proteins with the autophagy receptor TP53INP2/DOR

ABSTRACT The Atg8-family proteins (MAP1LC3/LC3A, LC3B, LC3C, GABARAP, GABARAPL1 and GABARAPL2) play a pivotal role in macroautophagy/autophagy through their ability to help form autophagosomes. Although autophagosomes form in the cytoplasm, nuclear levels of the Atg8-family proteins are significant. Recently, the nuclear/cytoplasmic shuttling of LC3B was shown to require deacetylation of two Lys residues (K49 and K51 in LC3B), which are conserved in Atg8-family proteins. To exit the nucleus, deacetylated LC3B must bind TP53INP2/DOR (tumor protein p53 inducible nuclear protein 2) through interaction with the LC3-interacting region (LIR) of TP53INP2 (TP53INP2LIR). To examine their selectivity for TP53INP2 and the role of the conserved Lys residues in Atg8-family proteins, we prepared the six human Atg8-family proteins and acetylated variants of LC3A and GABARAP for biophysical and structural characterization of their interactions with the TP53INP2LIR. Isothermal titration calorimetry (ITC) experiments demonstrate that this LIR binds preferentially to GABARAP subfamily proteins, and that only acetylation of the second Lys residue reduces binding to GABARAP and LC3A. Crystal structures of complexes with GABARAP and LC3A (acetylated and deacetylated) define a β-sheet in the TP53INP2LIR that determines the GABARAP selectivity and establishes the importance of acetylation at the second Lys. The in vitro results were confirmed in cells using acetyl-mimetic variants of GABARAP and LC3A to examine nuclear/cytoplasmic shuttling and colocalization with TP53INP2. Together, the results demonstrate that TP53INP2 shows selectivity to the GABARAP subfamily and acetylation at the second Lys of GABARAP and LC3A disrupts key interactions with TP53INP2 required for their nuclear/cytoplasmic shuttling.

Probing noncovalent binding, spectroscopic characteristics and antiproliferative behavior of inclusion complex between quinoline and para-sulfonatothiacalix[4]arene

The inclusion complex between bowl-shaped para-sulfonatothiacalix[4]arene (TSCX4) macrocycle and quinoline has been studied with a unison of UV–visible, infra-red, flourescence emission and 1H nuclear magnetic resonance (NMR) and 2D nuclear overhauser effect spectroscopy (NOESY), high resolution mass spectrometry (HRMS) experiments. Both 1H NMR titration and HRMS experiments point to 1:1 stoichiometry for the water soluble Q⊂TSCX4 complex. The electronic structure of the inclusion complex obtained from density functional theory (DFT) showed a partial encapsulation of quinoline guest, which is held within the host cavity by C–H---π, π---π and hydrogen bonding interactions. The fluorescence emission spectra upon complexation display marginal blue shift of the 411 nm band in TSCX4. Moreover, the binding constant (7.1 × 103 M−1) determined from fluoresence emission experiments underline the effective host–guest binding in the complex, which was corroborated through frequency up-shift (‘blue shift’) of characteristic Ar-OH (3433 cm−1) and SO3- vibrations (1141 cm−1 and 1037 cm−1) in the measured infrared spectra of TSCX4. The antiproliferative activitities of the Q⊂TSCX4 complex against HeLA, MDA-MB-231and N2a cells are presented. The Q⊂TSCX4 complex has been shown to be efficient against N2a (neuroblastoma) cell line.

Structure prediction of protein-ligand complexes from sequence information with Umol

Protein-ligand docking is an established tool in drug discovery and development to narrow down potential therapeutics for experimental testing. However, a high-quality protein structure is required and often the protein is treated as fully or partially rigid. Here we develop an AI system that can predict the fully flexible all-atom structure of protein-ligand complexes directly from sequence information. We find that classical docking methods are still superior, but depend upon having crystal structures of the target protein. In addition to predicting flexible all-atom structures, predicted confidence metrics (plDDT) can be used to select accurate predictions as well as to distinguish between strong and weak binders. The advances presented here suggest that the goal of AI-based drug discovery is one step closer, but there is still a way to go to grasp the complexity of protein-ligand interactions fully. Umol is available at: https://github.com/patrickbryant1/Umol.

Structural Diversity and Rare η1 Cu-C Interactions in CuI Complexes of 1,2,3-Triazole-Functionalized Bisphosphines.

This manuscript describes the synthesis of copper complexes of 1,2,3-triazolyl-phosphines: o-Ph2P(C6H4){1,2,3-N3CC6H5)C(PPh2)} (L1), (C6H5){1,2,3-N3C(C6H4(o-PPh2))-C(PPh2)} (L2), 3-Ph2P(C5H3N){1,2,3-N3C(C6H5)C(PPh2)} (L3), o-Ph2P(C6H4){1,2,3-N3C(C5H5N)C(PPh2)} (L4), and {(3,5-Ph2PC6H4-o)21,2,3-N3CCH} (L5). The reactions of L1-L3 with CuI salts afforded dimeric complexes having the general formula [Cu2(μ -X)2L2] (L = L1, X = Cl, Br and I: 1 - 3; L= L2, X = Cl, Br and I: 4- 6; L = L3; X = Cl, Br, and I: 7-9). The reaction of L4 with CuI in a 1:2 molar ratio afforded 1D-coordination polymer [{(CuI)2{o-Ph2P(C6H4){1,2,3-N3C(C5H5N)C(PPh2)}-μ-((k1-N)(k2-P,P))}}]n (10). The reaction of L5 with cuprous halides (CuX) (X = Br, I) yielded mononuclear complexes [CuX{(3,5-Ph2PC6H4-o)21,2,3-N3CCH}-κ2P,P] (X = Br, 12; I, 13). Crystal structures of complexes 12 and 13 showed close interactions between CuI and the triazole C7 carbon. These relatively short Cu···C7 separations may be due to the η1-C interaction (dπ-pπ bond) between the triazolic carbon atom (via pz orbital) and CuI or three-centered two-electron interaction between CuI and the triazolic C-H bond. The existence of the Cu···C interaction was further evinced by the QTAIM analysis in compounds 12 and 13.

Synthesis and characterization of novel quinaldic acid based Ni, Fe, and Cr Complexes: A computational and experimental study

Complexes ([Ni(quin-2-c)2(H2O)2]•2H2O, [Fe(quin-2-c)2(H2O)2], [Cr(quin-2-c)2(H2O)2] were synthesized from aqueous solutions of metal salts, quinaldic acid, and semicarbazide. In the crystal structure of the first complex, the nickel atom is chelated by the deprotonated quinaldic acid molecule through the oxygen atom of the carboxyl group, and the heterocyclic nitrogen atom, as well as two water molecules, are coordinated. The other two water molecules are located in the outer sphere. In the structure of the iron and chromium complexes, the metal atoms have a similar complex formation but do not have water molecules in the outer sphere. In all compounds, quinaldic acid acts as a bidentate ligand to form five-membered metallocycles. The electronic structure properties were investigated through theoretical modeling using the B3LYP method at the 6–31 + G(d,p) computational level. Density functional theory (DFT) was employed in quantum chemistry simulations to refine proposed structures and explore the characteristics of frontier orbitals via analysis of frontier molecular orbitals (FMOs). These computations facilitated the identification of specific sites on the surface of molecules by generating molecular electrostatic potential maps and provided insights into the structural and reactive properties. Hirshfeld surface analysis was conducted to examine intermolecular interactions, revealing a prevalence of H⋅⋅⋅H interactions.