Carbon dioxide adsorption thermodynamics in the metal–organic framework CALF‐20, a hydrothermally stable candidate for carbon capture, are predicted using two complementary approaches. An analytical ab initio thermodynamics method combines periodic density functional theory + dispersion interactions (DFT + D) with MP2 corrections for adsorption energies, local sampling of the potential energy surface, and a nonisolated‐site term to capture nonlocal effects. Grand Canonical Monte Carlo (GCMC) simulations using a newly developed force field enable comprehensive sampling of global configurations. Both methods reproduce experimental adsorption isotherms and heats of adsorption within chemical accuracy (±4 kJ mol−1). Dispersion dominates CO2 binding (>80%), while quantum effects on nuclear motion (zero‐point vibrational energy) contribute up to 5.4 kJ mol−1 to adsorption thermodynamics—impacting both adsorption enthalpies and Gibbs free energies. Nonlocal effects reduce entropy penalties by ≳7 kJ mol−1, yielding adsorption Gibbs free energies that reveal a two‐step pore filling mechanism: initial single occupancy of cages followed by intracage pairing. Triple cross‐validation across ab initio, GCMC, and experiment confirms this cooperative two‐step mechanism and reinforces the reliability of the thermodynamic dataset. This transferable strategy enables predictive modeling of adsorption thermodynamics in nanoporous materials for next‐generation carbon‐capture applications.

Hydantoin derivatives represent a versatile class of heterocycles, known for their pharmacological properties. Because drug efficacy often depends on the fine-tuning of weak intermolecular (non-covalent) interactions, analysis of the crystal structure of a drug molecule is important, as it enables deciphering its interaction profile. In this study, the crystal packing of phenytoin and its selected derivatives were examined through dimeric motifs with different recognition modes using force-field calculations and a density functional theory (DFT) approach. The relatively polar ethoxyacetyl group at the N3 position of the hydantoin ring, capable of forming hydrogen bonds, enhances the contribution of electrostatic and polar components to the total interaction energy. In contrast, the long alkyl chain promotes hydrophobic contacts, leading to dispersion forces dominating over electrostatic interactions. The reactivity of phenytoin and its derivatives were further evaluated by examining the influence of these substituents using conceptual density functional theory (CDFT) descriptors. These findings demonstrate that substituents significantly affect crystal packing and the balance of non-covalent interactions, providing valuable insights for optimizing molecular recognition and drug-target interactions in the design of new therapeutic agents.

Proper simulation of the structure and dynamics of large molecular systems rests on accurate and reliable force fields (FF) which can reproduce their behavior both in the gas phase and in condensed phases at a reasonable computational cost. The analytic potential energy functions are at the heart of force field based molecular simulations. The complexity of these functions spans the range from very simple functions used to model generic phenomena to complex functions designed to model chemical reactions. In this chapter, after a summary, we have selected several approaches, which we present and discuss in more detail.

The removal of highly toxic gasses such as SO2 and H2S is important in various industrial and environmental applications. Metal organic frameworks (MOFs) are promising candidates for the capture of toxic gases owing to their favorable properties such as high selectivity, moisture stability, thermostability, acid gas resistance, high sorption capacity, and low-cost regenerability. In this study, we perform first principles density functional theory (DFT) and grand-canonical Monte Carlo (GCMC) simulations to investigate the capture of highly toxic gases, SO2 and H2S, by the recently designed ZTF and MAF-66 MOFs. Our results indicate that ZTF and MAF-66 show good adsorption performances for SO2 and H2S capture. The nature of the interactions between H2S or SO2 and the pore surface cavities was examined at the microscopic level. SO2 is adsorbed on the pore surface through two types of hydrogen bonds, either between O of SO2 with the closest H of the triazole 5-membred ring or between O of SO2 with the hydrogen of the amino group. For H2S inside the pores, the principal interactions between H2S and surface pores are due to a relatively strong hydrogen bonds established between the nitrogens of the organic part of MOFs and H2S. Also, we found that these interactions depend on the orientation of SO2/H2S inside the pores. Moreover, we have studied the influence of the presence of water and CO2 on H2S and SO2 capture by the ZTF MOF. The present GCMC simulations reveal that the addition of H2O molecules at low pressure leads to an enhancement of the H2S adsorption, in agreement with experimental findings. However, the presence of water molecules decreases the adsorption of SO2 irrespective of the pressure used. Besides, SO2 adsorption is increased in the presence of a small number of CO2 molecules, whereas the presence of carbon dioxide in ZTF pores has an unfavorable effect on the capture of H2S.

Green corrosion inhibitors, Ce(III) chloride, Ce(III) nitrate, and Ce(III) propionate, were tested in NaCl solution with the aim to evaluate their inhibitory effect on 7049 aluminum alloy and to propose a mechanism of their inhibitive action. Corrosion properties of the formed inhibitor layer were analyzed using electrochemical impedance spectroscopy, while the pit formation resistance was analyzed using potentiodynamic polarization tests. Morphology of the formed pits was evaluated by scanning electron microscope/energy‐dispersive spectroscopy analysis. It was shown that Ce(III) propionate in NaCl solution has a noticeably higher protective ability than Ce(III) chloride and Ce(III) nitrate. The presence of cerium, propionate anions, and Al–O bonds in the inhibitive layer on the 7049 aluminum alloy surface was confirmed by X‐ray photoelectron spectroscopy analysis. This indicates the formation of Ce propionate complexes and bonds via oxygen atoms from carboxylate anions with the metal surface. Density‐functional theory methods were used for the geometry optimization of possible Ce propionate complexes as corrosion inhibitors.

of two 4-substituted N,N'-diphenyl-urea or N,N'-diphenyl-thiourea with one central squaraine molecule.Using different substituents in position 4 of phenyl the acidity of the N-H protons can be varied.In the second paper, the effect of a confining environment on the IR spectra of two hydrogen-bonded 50 intermolecular complexes, namely HCN -HCN and HCN -HNH, is studied by (Chołuj et al., 2022).The spatially confining environment is simulated by embedding the complexes in an external cylindrical 52 harmonic oscillator potential, and the harmonic frequencies are computed with high-level ab-initio methodsThe simulated confinement leads to substantial changes of both transition intensities and vibrational 54 frequencies.In the third study, (Szczesniak and Chalasinski, 2022), report an interesting analysis of a number of

HIV protease inhibitors are one of the most important agents for the treatment of HIV infection. In this work, molecular modeling studies combining 3D-QSAR, molecular docking, MESP, HOMO, and LUMO energy calculations were performed on propiophenone derivatives to explore structure activity relationships and structural requirements for the inhibitory activity. The aim of this study was to create a field point–based 3D-QSAR (3D-Quantitative structure-activity relationship) model by using chalcone structures with anti-HIV-1 protease activity from our previous study and to design new potentially more potent and safer inhibitors. The developed model showed acceptable predictive and descriptive capability as represented by standard statistical parameters R2 (0.94) and Q2 (0.59). High correlation between experimental and predicted activities of training set is noticed. All compounds fit into the defined applicability domain. The derived pharmacophoric features were further supported by MESP and Mulliken charge analysis using density functional theory. Statistically significant variables from 3D-QSAR were used to define key structural characteristics which enhance anti-HIV-1 protease activity. This information has been used to design new structures with anti-HIV-1 protease activity. Docking studies were conducted to understand the interactions in predicted compounds. All the compounds were subjected to in silico ADMET profiling in order to select the best potential drug candidates.

In search for future good adsorbents for CO2 capture, a nitrogen-rich triazole-type Metal-Organic Framework (MOF) is proposed based on the rational design and theoretical molecular simulations. The structure of the proposed MOF, named Zinc Triazolate based Framework (ZTF), is obtained by replacing the amine-organic linker of MAF-66 by a triazole, and its structural parameters are deduced. We used grand-canonical Monte Carlo (GCMC) simulations based on generic classical force fields to correctly predict the adsorption isotherms of CO2 and H2O. For water adsorption in MAF-66 and ZTF, simulations revealed that the strong hydrogen bonding interactions of water with the N atoms of triazole rings of the frameworks are the main driving forces for the high adsorption uptake of water. We also show that the proposed ZTF porous material exhibits exceptional high CO2 uptake capacity at low pressure, better than MAF-66. Moreover, the nature of the interactions between CO2 and the MAF-66 and ZTF surface cavities was examined at the microscopic level. Computations show that the interactions occur at two different sites, consisting of Lewis acid-Lewis base interactions and hydrogen bonding, together with obvious electrostatic interactions. In addition, we investigated the influence of the presence of H2O molecules on the CO2 adsorption on the ZTF MOF. GCMC simulations reveal that the addition of H2O molecules leads to an enhancement of the CO2 adsorption at very low pressures but a reduction of this CO2 adsorption at higher pressures.

Two new Zn(II) complexes with tridentate hydrazone-based ligands (condensation products of 2-acetylthiazole) were synthesized and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy and single crystal X-ray diffraction methods. The complexes 1, 2 and recently synthesized [ZnL3(NCS)2] (L3 = (E)-N,N,N-trimethyl-2-oxo-2-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)ethan-1-aminium) complex 3 were tested as potential catalysts for the ketone-amine-alkyne (KA2) coupling reaction. The gas-phase geometry optimization of newly synthesized and characterized Zn(II) complexes has been computed at the density functional theory (DFT)/B3LYP/6–31G level of theory, while the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO and LUMO) energies were calculated within the time-dependent density functional theory (TD-DFT) at B3LYP/6-31G and B3LYP/6-311G(d,p) levels of theory. From the energies of frontier molecular orbitals (HOMO–LUMO), the reactivity descriptors, such as chemical potential (μ), hardness (η), softness (S), electronegativity (χ) and electrophilicity index (ω) have been calculated. The energetic behavior of the investigated compounds (1 and 2) has been examined in gas phase and solvent media using the polarizable continuum model. For comparison reasons, the same calculations have been performed for recently synthesized [ZnL3(NCS)2] complex 3. DFT results show that compound 1 has the smaller frontier orbital gap so, it is more polarizable and is associated with a higher chemical reactivity, low kinetic stability and is termed as soft molecule.

Using a first-principle methodology, we investigate the stable structures of the nonreactive and reactive clusters formed between Zn2+-triazoles ([Zn2+-Tz]) clusters and CO2 and/or H2O. In sum, we characterized two modes of bonding of [Zn2+-Tz] with CO2/H2O: the interaction is established through (i) a covalent bond between Zn2+ of [Zn2+-Tz] and oxygen atoms of CO2 or H2O and (ii) hydrogen bonds through N-H or C-H of [Zn2+-Tz] and oxygen atoms of H2O or CO2, N-H···O. We also identified intramolecular proton transfer processes induced by complexation. Indeed, water drastically changes the shape of the energy profiles of the tautomeric phenomena through strong lowering of the potential barriers to tautomerism. The comparison to [Zn2+-Im] subunits formed with Zn2+ and imidazole shows that the efficiency of Tz-based compounds for CO2 capture and uptake is due to the incorporation of more accessible nitrogen donor sites in Tzs compared to imidazoles. Since [Zn2+-Tz] clusters are subunits of an organometallic nanoporous materials and Zn-proteins, our data are useful for deriving force fields for macromolecular simulations of these materials. Our work also suggests the consideration of traces of water to better model the CO2 sequestration and reactivity on macromolecular entities such as pores or active sites.

In search for antitumor metal-based drugs that would mitigate the severe side-effects of cisplatin, Ru(II) complexes are gaining increasing recent interest. In this work, we report on the synthesis, characterization (H-1- and C-13-NMR, FT-IR), and cytotoxicity studies of two new half-sandwich organometallic Ru(II) complexes of the general formula [Ru(eta(6)-arene)(XY)Cl](PF6) where arene = benzene or toluene and XY = bidentates: dipyrido[3,2-a:2 ',3 '-c]phenazine (dppz) or 2-(9-anthryl)-1H-imidazo[4,5-f][1,10]phenanthroline (aip), which are bound to Ru(II) via two phenanthroline-N atoms in a characteristic "piano-stool" configuration of Ru(II)-arene complexes-as confirmed by vibrational and NMR spectra. In addition, cytotoxic studies were performed for similar half-sandwich organometallic [Ru(eta(6)-p-cymene)(Me(2)dppz)Cl]PF6 complex (Me(2)dppz = 11,12-dimethyl-dipyrido[3,2-a:2 ',3 '-c]phenazine). This study is complemented with elaborate modeling with density functional theory (DFT) calculations, which provided insight into reactive sites of Ru(II) structures, further detailed by molecular docking on the B-DNA dodecamer, which identified binding sites and affinities: most pronounced for the [Ru(eta(6)-benzene)(aip)Cl](PF6) in both A-T and G-C regions of the DNA minor groove. Cytotoxic activity was probed versus tumor cell lines B16, C6, and U251 (B16 mouse melanoma, C6 rat glioma, U251 human glioblastoma) and non-tumor cell line HACAT (HACAT normal human keratinocytes). [GRAPHICS] .

The novel approach in the treatment of complex multifactorial diseases, such as neurodegenerative disorders and cancer, requires a development of efficient multi-targeting oriented drugs. Since oxidative stress significantly contributes to the pathogenesis of cancer and neurodegenerative disorders, potential drug candidates should possess good antioxidant properties. Due to promising biological activities shown for structurally related (1,3-thiazol-2-yl)hydrazones, a focused library of 12 structurally related benzylidene-based (1,3-selenazol-2-yl)hydrazones was designed as potential multi-targeting compounds. Monoamine oxidases (MAO) A/B inhibition properties of this class of compounds have been investigated. Surprisingly, the p-nitrophenyl-substituted (1,3-selenazol-2-yl)hydrazone 4 showed MAO B inhibition in a nanomolar concentration range (IC50 = 73 nM). Excellent antioxidant properties were confirmed in a number of different in vitro assays. Antiproliferative activity screening on a panel of six human solid tumor cell lines showed that potencies of some of the investigated compounds was comparable or even better than that of the positive control 5-fluorouracil. In-silico calculations of ADME properties pointed to promising good pharmacokinetic profiles of investigated compounds. Docking studies suggest that some compounds, compared to positive controls, have the ability to strongly interact with targets relevant to cancer such as 5'-nucleotidase, and to neurodegenerative diseases such as the small conductance calcium-activated potassium channel protein 1, in addition to confirmation of inhibitory binding at MAO B.

The mixed chloride-azide [ZnL(N3)1.65Cl0.35] (1) and chloride-isocyanate [CdL(NCO)1.64Cl0.36] (2) complexes with the condensation product of 2-quinolinecarboxaldehyde and trimethylammonium acetohydrazide chloride (Girard's T reagent) (HLCl) have been prepared and characterized by X-ray crystallography. In complexes 1 and 2, Zn1 and Cd1 ions, respectively, are five-coordinated in a distorted square based pyramidal geometry with NNO set of donor atoms of deprotonated hydrazone ligand and two monodentate ligands N3− and/or N3− and Cl− in the case of 1 and OCN− and/or OCN− and Cl− in the case of 2. The structural parameters of 1 and 2 have been discussed in relation to those of previously reported M(II) complexes with the same hydrazone ligand. Density functional theory calculations have been employed to study the interaction between the Zn2+ and Cd2+ ions and ligands. High affinity of ligands towards the Zn2+ and Cd2+ ions are predicted for both complexes.

Selenium has been increasingly recognized as an important element in biological systems, which participates in numerous biochemical processes in organisms, notably in enzyme reactions. Selenium can substitute sulfur of cysteine and methionine to form their selenium analogues, selenocysteine (Sec) and selenomethionine (SeM). The nature of amino acid pockets in proteins is dependent on their composition and thus different non-covalent forces determine the interactions between selenium of Sec or SeM and other functional groups, resulting in specific biophysical behavior. The discrimination of selenium toward sulfur has been reported. In order to elucidate the difference between the nature of S-π and Se-π interactions, we performed extensive DFT calculations of dispersive and electrostatic contributions of Se-π interactions in substituted benzenes/hydrogen selenide (H2Se) complexes. The results are compared with our earlier reported S-π calculations, as well as with available experimental data. Our results show a larger contribution of dispersive interactions in Se-π systems than in S-π ones, which mainly originate from the attraction between Se and substituent groups. We found that selenium exhibits a strong interaction with aromatic systems and may thus play a significant role in stabilizing protein folds and protein–inhibitor complexes. Our findings can also provide molecular insights for understanding enzymatic specificity discrimination between single selenium versus a sulfur atom, notwithstanding their very similar chemical properties.

Cobalt(III) complexes derived from thio-and selenosemicarbazone ligands have been studied to elucidate the nature and consequences of S to Se substitution on their possible biological activity. Solid state structures of cobalt(III) complexes with bis-tridentate coordinated 2-quinolinecarboxaldehyde thio-and selenosemicarbazone were determined by single crystal X-ray diffraction analysis. The complexes were also characterized by spectroscopic methods and cyclic voltammetry. Electronic properties of the complexes were studied using DFT and TD-DFT methods. Finally, evident in vitro antioxidant activity of the complexes was demonstrated.

The first Co(iii) complexes with (1,3-selenazol-2-yl)hydrazones as an unexplored class of ligands were prepared and characterized by NMR spectroscopy and X-ray diffraction analysis. The novel ligands act as NNN tridentate chelators forming octahedral Co(iii) complexes. The impact of structural changes on ligands' periphery as well as that of isosteric replacement of sulphur with selenium on the electrochemical and electronic absorption features of complexes are explored. To support the experimental data, density functional theory (DFT) calculations were also conducted. Theoretical NMR chemical shifts, the relative energies and natural bond orbital (NBO) analysis are calculated within the DFT approach, while the singlet excited state energies and HOMO-LUMO energy gap were calculated with time-dependent density functional theory (TD-DFT). The electrophilic f- and nucleophilic f+ Fukui functions are well adapted to find the electrophile and nucleophile centres in the molecules. Both (1,3-selenazol-2-yl)- and (1,3-thiazol-2-yl)hydrazone Co(iii) complexes showed potent antimicrobial and antioxidant activity. A significant difference among them was a smaller cytotoxicity of selenium compounds.

A tridentate NNO condensation product of 2-quinolinecarboxaldehyde and Girard's T reagent (HLC1) in the presence of azide ions coordinates with cobalt(II) giving mononuclear azido Co(II) complex [CoHL (N-3)(3)](1) as a main product and dinuclear end-on azido bridged Co(II) complex [Co2L2(mu-(1,1)-N-3)(2)(N-3)(2)] (2) in traces. Crystal structures of both complexes were determined. Variable temperature magnetic susceptibility measurement studies of complex I showed that Co(II) cation is in the low-spin state with t(2g)(6)e(g)(1) (S = 1/2) configuration. DFT-BS calculations for complex 2 anticipated ferromagnetic type interaction between paramagnetic centers (J = 53 cm(-1)). (C) 2017 Elsevier Ltd. All rights reserved.

The chloro (1) and isocyanato (2) Cd(II) complexes with the condensation product of 2-quinolinecarboxaldehyde and trimethylammonium acetohydrazide chloride (Girard's T reagent) (HLCl) have been synthesized and characterized by elemental analysis, IR, and NMR spectroscopy. The crystal structure of chloro Cd(II) complex (1) was determined. In 1 and 2, coordination surrounding of Cd(II) consists of deprotonated hydrazone ligand coordinated through NNO-donor atoms and two monodentates at the rest of the coordination places. Quantum chemical calculations of the molecular structures and the relative stabilities of linkage isomers of the Cd(II) complex showed that the isomer with N-Cd-N coordination of OCN- is the most stable. The investigated Cd(II) complexes showed lower activity than standard antimicrobial drugs. [GRAPHICS] .

Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 310- and/or α-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i → i + 3 and i → i + 4 hydrogen bonds characterizing 310 and α-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides.