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 Structural ChemistryJournal Prestige (SJR): 0.504 Citation Impact (citeScore): 2Number of Followers: 1      Hybrid journal (It can contain Open Access articles) ISSN (Print) 1572-9001 - ISSN (Online) 1040-0400 Published by Springer-Verlag  [2469 journals]
• Initiating a new column: Foundation of structural science

PubDate: 2022-08-01

• Sidney Altman (1939–2022)—molecular biologist, discoverer of
catalytic properties of RNA

Abstract: Abstract Sidney Altman (1939-2022) was a physicist turned molecular biologist. He was born in Canada, studied at MIT and at the University of Colorado, and did his most important work at the MRC LMB and Yale University. He shared the 1989 Nobel Prize in Chemistry for the discovery of catalytic properties of RNA.
PubDate: 2022-08-01

tribute to Erwin Chargaff

Abstract: Abstract Linus Pauling pronounced the importance of complementarity in chemical structures and processes involving biological molecules. Erwin Chargaff’s discovery of base equivalence in DNA provided the most beautiful example of such complementarity. He taught us to appreciate both generalization and the understanding of minute differences in advancing science.
PubDate: 2022-08-01

• Revised structure of 2,13-dinitro-5,10,15,20-tetraphenylporphyrin. Inside
high-resolution NMR

Abstract: Abstract 5,10,15,20-Tetraphenylporphyrin-copper(II) complex when nitrated with 25% aqueous nitric acid in CHCl3 led to three β,β-substituted dinitro-isomers. One of the structures of products reported in the original paper was assigned incorrectly (as 2,8-dinitro-5,10,15,20-tetraphenylporphyrin derivative). Investigations using high-resolution NMR allowed to assign this compound (examined as demetallated free base) a different structure: 2,13-dinitro-5,10,15,20-tetraphenylporphyrin. These types of products, being practically unavailable by alternative methods, are attractive starting material for synthesis of more complex porphyrinoid moieties.
PubDate: 2022-08-01

• Molecular docking study of biocompatible enzyme interactions for removal
of indoxyl sulfate (IS), indole-3-acetic acid (IAA), and p-cresyl sulfate
(PCS) protein bound uremic toxins

Abstract: The removal of protein bound uremic toxins (PBUT) from kidney failure patients is an ongoing challenge, as this type of protein tightly binds to viral proteins like human serum albumin (HSA) and makes it difficult to remove during hemodialysis (HD). PBUTs bind to transport protein HSA by electrostatic interaction and/or van der Waals (VDW) forces in human blood, and the low concentrations that are found in plasma. High flux dialysis for PBUT clearance leads to back-filtration and significant loss off efficacy, that in turn are responsible for a high number of HD patient deaths. Therefore, the successful removal of PBUT will solve a crucial problem for HD patients by addressing key challenges and achieving improved HD performance, reducing morbidity rates, and prolonging survival. Continued concerns with toxicity and high concentration of PBUT, p-cresyl sulfate (PCS), indoxyl sulfate (IS), and indole- 3-acetic acid (IAA) were chosen as the investigative foci for this study. The goal was to develop an in depth understanding of the PBUT attachments to HSA chains, by examining the interactions between biocompatible enzymes with those of PBUT for potential removal. Laccases from trametes versicolor and melanocarpus albomyces were selected for this study. Molecular modeling docking was used to examine the interactions between HSA and PCS, IS, and IAA. In addition, interactions between laccases and the PBUTs were reviewed with the aim of gaining a clearer understanding of the functional group responsible for perceived interactions necessary for a more efficient removal. Comparison of the results suggested a favorable removal of PBUTs by fungal laccase from melanocarpus albomyces (3FU9) due to its tendency for polar interactions and the affinity energy. Once the results were ranked by affinity, they revealed that melanocarpus albomyces laccase and IAA have the highest binding affinity of − 7.4 kcal/mol. The carboxylic group of IAA plays a key role in the interaction with laccase enzyme 3FU9 and more IAA binding energy to HSA. Therefore, the major outcome of this research points to Laccase 3FU9 being capable of removing IAA. Graphical abstract
PubDate: 2022-08-01

• Acid-based analogs of certain water tetramers: an examination of some
crystal structures in the literature

Abstract: Abstract Chemical clusters with composition (H2nOn), (H2n+1On)+, and (H2n−1On)− with n = 4 are crystallographically known. Moreover, for each of those classes, there are documented examples in more than one stereochemical conformation. In this study, we consider the relation between their stereochemical characteristics in the solid and in their free form as fluids, by calculating their energies as crystallographically reported, as well as by energy optimization. Also, since accurate crystallographic studies provided these species in more than one geometrical isomer, quantum mechanical comparisons of their energies in crystalline and free molecular form are herein reported. Finally, for those in which energy minimization(s) resulted in stereochemical rearrangements, the new stereoisomer resulting is herein described. Quantum calculations show the molecular energy increases from deprotonated, to neutral, to protonated fragments. Energy optimization was carried out for each of the crystal structures studied, which allowed us to determine the structural relationship between the crystalline and free form of these fragments. Among these aquo-fragments, the most frequent structures were quadrangular and triangular motifs with either four or three hydrogen bonds. The quantum chemical calculated energy of all crystal and optimized structures are reported.
PubDate: 2022-08-01

• 3D-QSAR, ADME-Tox, and molecular docking of semisynthetic triterpene
derivatives as antibacterial and insecticide agents

Abstract: Abstract In the present work, 27 triterpene derivatives have been subjected to 3D-QSAR, ADME-Tox, and molecular docking for their insecticidal activity. The selected derivatives are previously semi-synthesized based on compounds obtained from Euphorbia resinifera and Euphorbia officinarum latex. The in silico studies were used to predict and to evaluate the antibacterial and insecticidal properties of the 3D structure of triterpene derivatives. The 3D-QSAR models are developed using CoMFA and CoMSIA techniques, and they have showed excellent statistical results (R2 = 0.99; Q2 = 0.672; R2pred = 0.91 for CoMFA and R2 = 0.97; Q2 = 0.61; R2pred = 0.94 for CoMSIA). The results indicate that the built models are able to describe the relationship between the structure of triterpene derivatives and the pLD50 bioactivity. Based on contour maps obtained from CoMFA and CoMSIA models, 38 new molecules are designed and their pLD50 activities are predicted. The drug-like and ADME-Tox properties of the molecule designed are examined and led to the selection of four molecules (55, 56, 59, 64) as promising antibacterial and insecticidal agents. Compounds 55, 56, 59, and 64 are able to inhibit the MurE (PDB code: 1E8C) and EcR (PDB code: 1R20) proteins involved in the process of antibacterial and insecticidal activities. This hypothesis is confirmed by the implementation of a molecular docking test. This test predicted the most important referential interactions that occur between the structure of triterpene derivatives and the targeted receptors. Among the four docked molecules, three molecules (55, 56, and 59) showed greater stability than the reference molecule 16 inside the MurE and EcR receptors pocket. Therefore, the structure of the three new triterpene derivatives can be adopted as reference for the synthesis of antibacterial drugs and also in the development of insecticides.
PubDate: 2022-08-01

• Insights into solvation, chemical reactivity, structural, vibrational and
anti-hypertensive properties of a thiazolopyrimidine derivative by DFT and
MD simulations

Abstract: Abstract In this study, a thiazolopyrimidine derivative ethyl 2-(2-acetoxyphenyl)-5-(4 (benzyloxy) phenyl)-7-methyl-3-oxo-3,5-dihydro-2H-thiazolo[3,2-a]pyrimidine-6 carboxylate (EAPC) was investigated experimentally and theoretically. FMOs (frontier molecular orbitals), MEP, ALIE surfaces and solvation free energies were calculated for EAPC at CAM-B3LYP/6–311++G(2d,p) level. Solvation free energies in water, ethanol, acetone, acetonitrile, and chloroform were obtained and the analysis of the energy values suggests that acetone and acetronitrile may be better for solubilization of EAPC. However, the value of solvation energy in water (hydration free energy) indicates good solubility of the studied molecule in an aqueous medium, factor that corroborates the biological activity. Vibrational analysis, together with potential energy distribution (PED) calculations, revealed several characteristic vibrations. Molecular docking and molecular dynamics simulations carreid out with angiotensin I-converting enzyme revealed that EAPC is a promising antihypertensive candidate.
PubDate: 2022-08-01

• Unveiling the nature of interactions in the supramolecular complex of
Cucurbit [7-8] uril with ascorbic acid, dopamine and uric acid for
biosensing applications: a computational study

Abstract: Abstract The selectivity and sensitivity in the detection of ascorbic acid, dopamine and uric acid is an open problem in the field of biosensing. The host-guest interactions of Cucurbit[n]uril (n=7, 8) as host and ascorbic acid (AA), dopamine (DA) and uric acid (UA) as the guest molecules has been studied using density functional theory with dispersion corrections. The energetic and thermodynamic results indicates that UA forms the most stable structure with CB7 and CB8 in gas phase. In aqueous phase, CB7 favours complexation with AA while CB8 favours DA. The non-covalent interactions that binds the supramolecular complexes are analyzed by molecular electrostatic potentials, non-covalent interactions-reduced density gradient and natural bond orbital analysis. Local energy decomposition (LED) analysis based on the non-perturbative natural orbital local domain (DLPNO)-CCSD(T) calculations is carried out for quantifying the intermolecular forces which stabilizes the complexes. The results indicate that the electrostatic interactions, van der Waals forces, intermolecular charge transfer interactions and intermolecular hydrogen bonding are responsible for the stabilization of the complexes. The study may be useful in designing Cucurbituril-based sensing device for these analytes.
PubDate: 2022-08-01

• Synthesis of the nickel(II) complexes bearing tetradentate
thiosemicarbazone through Michael addition of n-alcohols. Experimental,
theoretical characterization and antioxidant properties

Abstract: Abstract New thiosemicarbazone derivative, 3-benzylidene-2,4-pentanedione-S-methyl-thiosemicarbazone hydrogen iodide (TSC), was synthesized and characterized by elemental analysis, IR, 1H NMR and single crystal X-ray diffraction. The novel nickel(II) complexes, Ni1-4, were synthesized from the TSC and salicylaldehyde by template effect of nickel(II) ion. The reactions were accomplished by a proton provided from the addition of alcohols which are methyl, ethyl, propyl and allyl for complexes Ni1, 2, 3 and 4, respectively. Spectroscopic data indicated that the formation of the complexes occurred through Michael addition of the alcohols to the 2,4-pentanedione moiety of the TSC. Distorted square planar structures of complexes Ni1 and Ni2 were confirmed by single crystal X-ray diffraction. In addition, the detailed computations were performed by using the theory DFT for experimentally obtained structures of the TSC, Ni1 and Ni2. The antioxidant property of the TSC and nickel(II) complexes along with the standard ascorbic acid was studied by using DPPH radical scavenging and Cupric Reducing Antioxidant Capacity (CUPRAC) assays.
PubDate: 2022-08-01

• Structural, vibrational and thermodynamic properties of the isomers of the
dimer molecules Ba2X4 (X = F, Cl, Br, or I)

Abstract: Abstract Geometrical parameters and vibrational spectra of the dimer Ba2X4 molecules were calculated; different isomeric structures were revealed. For the Ba2F4, Ba2Cl4, and Ba2Br4, three isomers of C3v, C2v, and C2h symmetries were confirmed to exist while for Ba2I4 only two isomers, C3v and C2h, were confirmed. For all halides, the bipyramidal C3v isomers possessed the lowest energy. The structural parameters and vibrational frequencies were employed in calculation of thermodynamic functions and enthalpies of dissociation reactions of the species. The enthalpies of formation ∆fH(0) of the C3v isomers were obtained (in kJ mol−1): − 1874 ± 2 (Ba2F4); − 1236 ± 7 (Ba2Cl4); − 1023 ± 8 (Ba2Br4); − 787 ± 11 (Ba2I4). The relative abundance of the isomeric forms was evaluated for a broad temperature range, between 200 and 2000 K. It was shown that the concentrations of different isomers appeared to be comparable in saturated vapors at temperatures close to experimental conditions.
PubDate: 2022-08-01

• Computational investigation of thermal decomposition mechanism of
5-nitro-5-R-1,3-dioxane compounds

Abstract: Abstract This paper features the results of the computational study of thermal decomposition reaction of 5-nitro-5-R-1,3-dioxane compounds, with R = H, Br, and CH3. Computational calculations were performed with M06-2X, MPWB1K, PBE0 and ωB97X-D functionals, and 6–311 + G(d,p) basis set in gas phase and also in solution with DMSO, at different temperatures. The kinetic and thermodynamic data obtained indicate a favoring of the reaction when the molecule presents substituent groups in position 5 and when carried out in DMSO, the stability of the molecules in their energetic components was discussed, too. For R = H two different reaction mechanisms were proposed and studied. Wiberg bond indices were obtained for the reactions studied and the results were examined in terms of bond formation and bond breaking progress as well.
PubDate: 2022-08-01

• Investigation of structural, electronic, and antioxidant properties of
calycopetrin and xanthomicrol as two polymethoxylated flavones using DFT
calculations

Abstract: Abstract Calycopetrin (Cal) and xanthomicrol (Xan) are extracted from various plant sources as polymethoxylated flavones and have extraordinary biological properties. All structural, electronic, and spectral data of these two compounds such as HOMO, LUMO energies, electrophilicity index, molecular electrostatic potential maps, 1HNMR, and 13CNMR were obtained using B3LYP/6–31 + G(d, p) computational method and were examined and interpreted in detail. Their antioxidant properties were also evaluated by hydrogen atom transfer, single electron transfer followed by proton transfer, and the sequential proton loss electron transfer mechanisms in the gas phase and water and compared with phenol. Delocalization of odd electrons in the studied radicals was also investigated using spin density maps. Finally, the reactivity of Cal and Xan with oxygen radicals such as HO˚, HOO˚, and O2˚¯ was investigated.
PubDate: 2022-08-01

• Computational analysis of carbazole-based newly efficient D-π-A organic
spacer dye derivatives for dye-sensitized solar cells

Abstract: Abstract In this study, the newly designed organic dyes (CBS1-CBS3) were designed by the donor (D), π-linkers (π) and acceptor (A) to forming the D-π-A structure. Besides, the screened efficient spacer dye sensitizers were simulated by the density functional theory (DFT) and time-dependent DFT (TD-DFT) methods for dye-sensitized solar cell (DSSC) application. First, the optical absorption peak of CB1 dye was analyzed by the different exchange–correlation (XC) and long-range corrected (LC) functionals with 6-31G(d) basis set. As a result of functional, TD-CAM-B3LYP method nearly well matched with the literature data of CB1. The computational outcomes were shown that the highest occupied molecular orbitals (HOMOs) and lowest unoccupied MOs (LUMOs) of the CBS1-CBS3 dyes confirmed useful response on the electron injection ( $$\Delta {G}_{\text{inject}}$$ ) and dye regeneration ( $$\Delta {G}_{\text{reg}}$$ ). Therefore, the short-circuit current density ( $${J}_{\text{SC}}$$ ) key factors of the light harvesting efficiency (LHE), $$\Delta {G}_{\text{inject}}$$ and $$\Delta {G}_{\text{reg}}$$ in CBS1-CBS3 dye derivatives were superior performance of the DSSCs. In addition to the highest vertical dipole moment (µnormal) and open circuit photovoltage ( $$e{V}_{\text{OC}}$$ ) of the planned dyes were better performance for DSSCs. Hence, it benefits to higher efficiency. The present theoretical investigation results demonstrate that all the D-π-A dyes may be capable sensitizers for DSSC application.
PubDate: 2022-08-01

• Computational investigation of pyrrolidin derivatives as novel
GPX4/MDM2–p53 inhibitors using 2D/3D-QSAR, ADME/toxicity, molecular
docking, molecular dynamics simulations, and MM-GBSA free energy

Abstract: Abstract The p53 is a tumor suppressor protein that adjusts cell cycle and growth arrest as well as genes that restore DNA damage and apoptosis. Murine double minute 2 (MDM2) is a main p53 antagonist. We created a novel QSAR model using a series of highly active spiro [pyrrolidin-3,2-oxindoles] that consisted of 29 compounds that were experimentally validated to inhibit the MDM2-p53 interaction. Three optimal models have been developed CoMFA/E + S, CoMSIA/S + H + A, and HQSAR have revealed good statistical results, but the CoMSIA mode only which validates all the external validation tests applied successfully. Based on the CoMSIA/S + H + A model was carefully chosen to design four compounds with values of inhibitory activity greater than the highly active compound in the data set. The newly designed compounds were docked in the target receptor binding site (ID: 4LWU). The newly designed compound Pred 01 showed the highest affinity with a value of − 9.4 kcal/mol, while compound No. 04 which represents the data set and control compound (Nutlin-3) showed binding energies of the order of − 8.8 kcal/mol and − 8.2 kcal/mol, respectively. In addition, ADME/toxicity prediction and the drug-likeness predicted out of Lipinski’s rule and Veber’s rule were estimated; the results obtained demonstrate that the proposed molecules involve good oral bioavailability and an ability to diffuse through different biological barriers. For in-depth study, The Pred01/receptor, No. 04/receptor, and Nutlin-3/receptor complexes were selected via dynamic simulation analyzes with a simulation time of 100 ns and, also, their free binding energy was examined operating the MM-GBSA approach. The molecular docking results obtained accentuate the crucial residues responsible for the ligand/protein interaction, providing insight into the mode of interaction. The MD simulation analysis confirms the conformational stability of the selected complexes during the MD trajectory, and the fluctuations recorded are insignificant. The results of MM-GBSA reveal that the new compound Pred 01 exhibits the lowest free energy, which confirms the result of molecular docking.
PubDate: 2022-08-01

• Reversible coloring/decoloring reactions of thermochromic leuco dyes
controlled by a macrocyclic compound developer

Abstract: Abstract In this study, we examine macrocyclic compounds to determine whether they can provide a safer replacement and stable complex for BPA in thermochromic dyes. To achieve this objective, a series of macrocyclic compounds, Methyl-N-benzylhexahomotriazacalix[3]arene (MeAC3), p-Chloro-N-benzylhexahomo-triazacalix[3]arene (ClAC3), α-Cyclodexdrin (α-CD), β-Cyclodexdrin (β-CD), p-tert-Butylthiacalix[4]arene (TC4), Calix[4]arene (C4), and Resorcin[4]arene (RC4), were synthesized. Among these macrocyclic compounds, RC4 was determined to be the most appropriate candidate to replace BPA as the developer material used in thermochromic dyes. In tests of prepared thermochromic dyes, RC4 had results similar to those of BPA, achieving the best protonation/deprotonation equilibria and providing a dark contrast with the thermochromic dye. DFT calculations also showed stable complexes between RC4 and CVL via hydrogen-bond interactions.
PubDate: 2022-08-01

• DFT studies on the physicochemical properties of a new potential drug
carrier containing cellobiose units and its complex with paracetamol

Abstract: Abstract The formation of a carrier-drug complex may enhance the biodistribution of the drug and, consequently, improve its therapeutic effect. Since the biodistribution of the tied drug strongly depends on the properties of the carrier molecule, it is advisable to determine its structural features and other physicochemical parameters. Therefore, in this work, the properties of the new potential drug carrier 1,10-N,N’-bis-(β- $$\small{\text{D}}$$ -ureidocellobiosyl)-4,7,13-trioxa-1,10-diazacyclopentadecane (L2) were investigated using different quantum chemical methods. The most stable structures obtained from the B3LYP-GD2/6-31G(d,p) calculations have a very compact geometry due to the formation of intramolecular hydrogen bonds between the cellobiose fragments. The Mulliken charge distribution shows that L2 is strongly polar, so it is expected to bind efficiently polar molecules. The complexation ability of the host towards the polar drug paracetamol (PAR) in a stoichiometry 1:1 was investigated for various host-drug structures using the same density functional. The formation of L2:PAR is very profitable: for the most stable configuration, the complexation energy is −18.5 kcal/mol. In all structures, paracetamol is externally attached to the host, interacting mainly with the cellobiose units. The NMR chemical shifts obtained from the quantum calculations for L2 and its complex L2:PAR, are analyzed and compared with the available experimental data.
PubDate: 2022-08-01

• Synthesis, computational analyses, antibacterial and antibiofilm
properties of nicotinamide derivatives

Abstract: Abstract Newly designed nicotinamide derivatives were synthesized and characterized using spectral techniques (IR, 1H-NMR, 13C-NMR, and MS). Moreover, these compounds are investigated computationally. B3LYP/6–31 + G(d,p) level is selected as the calculation level in this study. Experimental and calculated IR spectrum were compared to each other. Electronic properties of synthesized compounds are examined using HOMO/LUMO contour plot and MEP maps. Antibacterial activity and antibiofilm properties are investigated experimentally. Additionally, antibacterial properties of studied compounds are investigated by molecular docking analyses. As a result, ND4 was found as the best inhibitor candidate against Enterococcus faecalis.
PubDate: 2022-08-01

• Theoretical investigation and reconsideration of intramolecular
proton-transfer-induced the twisted charge-transfer for the fluorescent
sensor to detect the aluminum ion

Abstract: Abstract A Schiff base compound 6-amino-5-(((2-hydroxynaphthalen-1-yl)methylene)amino)-2-mercaptopyrimidin-4-ol (AHM) in acetonitrile solvent is found to show “OFF–ON type” mode upon addition of Al3+ ion and successfully applied for selective recognition of Al3+ ion. In this work, the reconsideration of excited state intramolecular proton transfer (ESIPT) and twisted intramolecular charge transfer (TICT) has been explored in detail based on density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. In the absence of Al3+, the lone pair electrons are transferred from –C = N to –OH forming a hydrogen-bonding configuration, and AHM shows weak fluorescence. When AHM is coordinated with metal ion, the TICT state is eliminated, and emission is significantly enhanced. Thus, in this paper, the origination of the non-emissive behavior of AHM has been explained in detail. The frontier molecular orbitals (MOs) and hole-electrons are used to analyze the charge distribution, providing strong evidence for the possibility of ESIPT and TICT processes occurring.
PubDate: 2022-08-01

• Theoretical studies on structure and dynamics of anatase TiO2
(101)/H2SO4/H2O interface in the early stage of titania sulfation

Abstract: Abstract This work provides a molecular-level insight into the structural and dynamical processes of H2SO4/H2O molecules on anatase TiO2 (101) surface using the self-consistent-charge density-functional tight-binding molecular dynamics (SCC-DFTB/MD) method. The structural simulation model has been carried out at a constant temperature of 298.15 K for 20 ps. The integration algorithm used is velocity − verlet with Berendsen thermostat as a temperature controller. As a result, we find that radial distribution function (RDF) analyses exhibit the Ti5c-Os bond showing the highest peak at a distance of 2.02 Å, while the Ti-Ow bond is located at a distance of 2.1 Å. In the analysis of the number of bonds adsorbed on the surface of the titania, it was found that two bonds for Ti-Os and nine bonds for Ti-Ow were observed at the simulation time up to 20 ps. The proposed mechanism of sulfated titania formation is revealed via DFTB calculations. The obtained results suggest that the TiO2 surface is activated at Bronsted acid sites on the metal surface (Ot–Hs). Subsequently, the bisulfate ion is formed when a proton (H+) is lost from a deprotonated sulfuric acid molecule. Furthermore, this work is expected to give some light on the mechanism of sulfated titania formation and may provide some insights into the mechanisms of other superacid catalysts.
PubDate: 2022-08-01

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