Compromise in Docking Power of Liganded Crystal Structures of Mpro SARS-CoV-2 Surpasses 90% Success Rate.

Herein, we present the capacity of three different molecular docking programs (AutoDock, AutoDock Vina, and PLANTS) to identify and reproduce the binding modes of ligands present in 247 covalent and 169 noncovalent complex crystal structures of the severe acute respiratory syndrome coronavirus 2 main protease (Mpro). The compromise in docking power is evaluated with respect to their ability to generate poses similar to the crystal structure binding mode (heavy atoms' root-mean-square deviation < 2 Å) and their ability to recognize the native binding mode with an included compensation for the scoring function error. Noncovalently bound inhibitors are best modeled by AutoDock Vina (90.6% success rate in the active site), while the most relevant results for covalently bound inhibitors are produced by PLANTS (93.0%). AutoDock shows acceptable performance for both types of ligands, 81.1 and 76.4% for noncovalent and covalent complexes, respectively. All three programs manifest worse performance when reproducing surface-bound ligands. Comparison with other works illustrates the importance of crystal structure processing (12% of noncovalent and 26% of covalent ligands had to be manually corrected), proper sampling protocol settings, and inclusion of root-mean-square deviation (RMSD)/scoring function error compensations in crystal structure pose identification. Results are analyzed with respect to a clustering scheme of the noncovalently bound ligands and the chemical reaction type of the covalent ligand bound to the Cys145 residue. A comparison of screening power based on the docking scores of noncovalent ligands from the crystal structures with a "Directory of Useful Decoys, Enhanced" set of known decoys (6562 compounds) and ZINC15 in vivo subset (60,394 compounds) is provided. Ligand and protein input files are provided for future benchmarking purposes.

Isomerization pathway of a C-C sigma bond in a bis(octaazamacrocycle)dinickel(II) complex activated by deprotonation: a DFT study.

The anti (a) to syn (s) isomerization pathway of the deprotonated form of the dimer with two nickel(II) 15-membered octaazamacrocyclic units connected via a carbon-carbon (C-C) σ bond was investigated. For the initial anti (a) structure, a deprotonation of one of the bridging (sp3 hybridized) carbon atoms is suggested to allow for an a to s geometry twist. A 360° scan around the bridging C-C dihedral angle was performed first to find an intermediate geometry. Subsequently, the isomerization pathway was explored via individual steps using a series of mode redundant geometry optimizations (internal coordinates potential energy surface scans) and geometry relaxations leading to the s structure. The prominent geometries (intermediates) of the isomerization pathway are chosen and compared to the a and s structures, and geometry relaxations of the protonated forms of selected intermediates are considered. Supplementary Information: The online version contains supplementary material available at 10.1007/s00214-024-03100-5.

The Ruthenium Nitrosyl Moiety in Clusters: Trinuclear Linear µ-Hydroxido Magnesium(II)-Diruthenium(II), µ3-Oxido Trinuclear Diiron(III)-Ruthenium(II), and Tetranuclear µ4-Oxido Trigallium(III)-Ruthenium(II) Complexes.

The ruthenium nitrosyl moiety, {RuNO}6, is important as a potential releasing agent of nitric oxide and is of inherent interest in coordination chemistry. Typically, {RuNO}6 is found in mononuclear complexes. Herein we describe the synthesis and characterization of several multimetal cluster complexes that contain this unit. Specifically, the heterotrinuclear µ3-oxido clusters [Fe2RuCl4(µ3-O)(µ-OMe)(µ-pz)2(NO)(Hpz)2] (6) and [Fe2RuCl3(µ3-O)(µ-OMe)(µ-pz)3(MeOH)(NO)(Hpz)][Fe2RuCl3(µ3-O)(µ-OMe)(µ-pz)3(DMF)(NO)(Hpz)] (7·MeOH·2H2O) and the heterotetranuclear µ4-oxido complex [Ga3RuCl3(µ4-O)(µ-OMe)3(µ-pz)4(NO)] (8) were prepared from trans-[Ru(OH)(NO)(Hpz)4]Cl2 (5), which itself was prepared via acidic hydrolysis of the linear heterotrinuclear complex {[Ru(µ-OH)(µ-pz)2(pz)(NO)(Hpz)]2Mg} (4). Complex 4 was synthesized from the mononuclear Ru complexes (H2pz)[trans-RuCl4(Hpz)2] (1), trans-[RuCl2(Hpz)4]Cl (2), and trans-[RuCl2(Hpz)4] (3). The new compounds 4-8 were all characterized by elemental analysis, ESI mass spectrometry, IR, UV-vis, and 1H NMR spectroscopy, and single-crystal X-ray diffraction, with complexes 6 and 7 being characterized also by temperature-dependent magnetic susceptibility measurements and Mössbauer spectroscopy. Magnetometry indicated a strong antiferromagnetic interaction between paramagnetic centers in 6 and 7. The ability of 4 and 6-8 to form linkage isomers and release NO upon irradiation in the solid state was investigated by IR spectroscopy. A theoretical investigation of the electronic structure of 6 by DFT and ab initio CASSCF/NEVPT2 calculations indicated a redox-noninnocent behavior of the NO ancillary ligand in 6, which was also manifested in TD-DFT calculations of its electronic absorption spectrum. The electronic structure of 6 was also studied by an X-ray charge density analysis.

3CLpro and PLpro affinity, a docking study to fight COVID19 based on 900 compounds from PubChem and literature. Are there new drugs to be found?

The spread of a novel coronavirus SARS-CoV-2 and a resulting COVID19 disease in late 2019 has transformed into a worldwide pandemic and has effectively brought the world to a halt. Proteases 3CLpro and PLpro, responsible for proteolysis of new virions, represent vital inhibition targets for the COVID19 treatment. Herein, we report an in silico docking study of more than 860 COVID19-related compounds from the PubChem database. Molecular dynamic simulations were carried out to validate the conformation stability of compound-ligand complexes with best docking scores. The MM-PBSA approach was employed to calculate binding free energies. The comparison with ca. 50 previously reported potential SARS-CoV-2's proteases inhibitors show a number of new compounds with excellent binding affinities. Anti-inflammatory drugs Montelukast, Ebastine and Solumedrol, the anti-migraine drug Vazegepant or the anti-MRSA pro-drug TAK-599, among many others, all show remarkable affinities to 3CLpro and with known side effects present candidates for immediate clinical trials. This study reports thorough docking scores summary of COVID19-related compounds found in the PubChem database and illustrates the asset of computational screening methods in search for possible drug-like candidates. Several yet-untested compounds show affinities on par with reported inhibitors and warrant further attention. Furthermore, the submitted work provides readers with ADME data, ZINC and PubChem IDs, as well as docking scores of all studied compounds for further comparisons.

Ni Oxidation State and Ligand Saturation Impact on the Capability of Octaazamacrocyclic Complexes to Bind and Reduce CO2.

Two 15-membered octaazamacrocyclic nickel(II) complexes are investigated by theoretical methods to shed light on their affinity forwards binding and reducing CO2. In the first complex 1[NiIIL]0, the octaazamacrocyclic ligand is grossly unsaturated (π-conjugated), while in the second 1[NiIILH]2+ one, the macrocycle is saturated with hydrogens. One and two-electron reductions are described using Mulliken population analysis, quantum theory of atoms in molecules, localized orbitals, and domain averaged fermi holes, including the characterization of the Ni-CCO2 bond and the oxidation state of the central Ni atom. It was found that in the [NiLH] complex, the central atom is reduced to Ni0 and/or NiI and is thus able to bind CO2 via a single σ bond. In addition, the two-electron reduced 3[NiL]2- species also shows an affinity forwards CO2.

Coordination bonding in dicopper and dichromium tetrakis(µ-acetato)-diaqua complexes: Nature, strength, length, and topology.

Geometry optimization, energetics, electronic structure, and topology of electron density of dicopper (I) and dichromium (II) tetrakis(µ-acetato)-diaqua complexes are studied focusing on the metal-metal interactions. The performance of broken symmetry (BS) single-determinant ab initio (Hartree-Fock, Møller-Plesset perturbation theory to the second and third orders, coupled clusters singles and doubles) and density functional theory (BLYP, B3LYP, B3LYP-D3, B2PLYP, MPW2PLYP) methods is compared to multideterminant ab initio (CASSCF, NEVPT2) methods as well as to the multipole model of charge density from a single-crystal X-ray diffraction experiment (Herich et al., Acta Cryst. 2018, B74, 681-692). In vacuo DFT geometry optimizations (improper axial water ligand orientation) are compared against the periodic ones. The singlet state is found to be energetically preferred. J coupling of (I) becomes underestimated for all ab initio methods used, when compared to experiment. It is concluded that the strength of the direct M─M interactions correlates closely with the J coupling magnitude at a given level of theory. The double potential well character of (II) and of the dehydrated form of (II) are considered with respect to the Cr─Cr distance. The physical effective bond order of the metal-metal interaction is small (below 0.1 e) in (I) and moderate (0.4 e) in (II). The CASSCF results overestimate the electron density of the metal-metal bond critical point by 20% and 50% in (I) and (II), respectively, when compared to the multipole model. © 2019 Wiley Periodicals, Inc.

High-Frequency and -Field EPR (HFEPR) Investigation of a Pseudotetrahedral CrIV Siloxide Complex and Computational Studies of Related CrIVL4 Systems.

Chromium species are the active sites in a variety of heterogeneous catalysts, such as the Phillips catalyst, which is composed of Cr ions supported by SiO2 and is used to produce polyethylene. Among the catalytically relevant oxidation states of chromium is CrIV. Families of neutral, homoleptic, four-coordinate complexes, CrL4, with a variety of monoanionic, monodentate ligands, such as L = alkyls, aryls, amides, ketimides (R2C = N-), alkoxides, and siloxides, are available and can provide information regarding Cr sites in heterogeneous materials. For example, the previously reported siloxide, Cr(DTBMS)4, where DTBMS = -OSiMe tBu2 (di- tert-butylmethylsiloxide), may be considered a molecular analogue of CrIV supported by SiO2. Such CrL4 complexes can have either a singlet ( S = 0) or triplet ( S = 1) spin ground state, and the spin state preferences of such complexes are not fully understood. A truly tetrahedral d2 S = 1 complex would exhibit no zero-field splitting (zfs), and the zfs is indeed small and observable by X-band EPR for several CrR4 and Cr(OR)4 complexes. In contrast, Cr(DTBMS)4 has zfs beyond the range amenable to X-band EPR so that high-frequency and high-field EPR (HFEPR) is appropriate. HFEPR of Cr(DTBMS)4 in the solid state shows the presence of three very similar triplet species with the major component having D = +0.556 cm-1. Classical ligand-field theory (LFT) and quantum chemical theory (QCT), including ab initio methods, use EPR and electronic absorption spectra to give a complete picture of the electronic structure of Cr(DTBMS)4, and other complexes of formula Cr(ER n)4, E = C, n = 3; E = N, n = 2; E = O, n = 1; E = F, n = 0. Computations show the importance of ligand steric bulk and of π-bonding in controlling the subtleties of electronic structure of CrL4 species. These electronic structure results, including zfs, which is a measure of excited state accessibility, for both triplet and singlet excited states, might be related to the catalytic activity of paramagnetic Cr species.

Nickel(II) Complexes with Redox Noninnocent Octaazamacrocycles as Catalysts in Oxidation Reactions.

Nickel(II) complexes with 15-membered (1-5) and 14-membered (6) octaazamacrocyclic ligands derived from 1,2- and 1,3-diketones and S-methylisothiocarbohydrazide were prepared by template synthesis. The compounds were characterized by elemental analysis, electrospray ionization mass spectrometry, IR, UV-vis, 1H NMR spectroscopies, and X-ray diffraction. The complexes contain a low-spin nickel(II) ion in a square-planar coordination environment. The electrochemical behavior of 1-6 was investigated in detail, and the electronic structure of 1e-oxidized and 1e-reduced species was studied by electron paramagnetic resonance, UV-vis-near-IR spectroelectrochemistry, and density functional theory calculations indicating redox noninnocent behavior of the ligands. Compounds 1-6 were tested in the microwave-assisted solvent-free oxidation of cyclohexane by tert-butyl hydroperoxide to produce the industrially significant mixture of cyclohexanol and cyclohexanone (i.e., A/K oil). The results showed that the catalytic activity was affected by several factors, namely, reaction time and temperature or amount and type of catalyst. The best values for A/K oil yield (23%, turnover number of 1.1 × 102) were obtained with compound 6 after 2 h of microwave irradiation at 100 °C.

Impact of Substituent Variation on the Presence of Thermal Spin Crossover in a Series of Mononuclear Iron(III) Schiff Base Complexes with Terminal Pseudohalido Co-ligands.

A series of novel iron(III) complexes of the general formula [Fe(L)X] (where L is a dianion of pentadentate Schiff base ligand N,N'-bis({2-hydroxy-3,5-dimethylphenyl}phenyl)methylidene-1,6-diamino-3-azapentane=H2 L1 for 1 and 2; N,N'-bis({2-hydroxy-3-ethoxyphenyl}methylidene)-1,6-diamino-3-azapentane=H2 L2 for 3 and 3⋅C3 H6 O) and X is terminal pseudohalido ligand (X=N3 for 1, X=NCS for 2, and X=NCSe for 3 and 3⋅C3 H6 O) were synthesized and thoroughly characterized. Magnetic measurements revealed the above room temperature spin crossover for isomorphic complexes 1 and 2 (T1/2 =441 K and T1/2 =435 K, respectively), whereas the solvent-free complex 3 showed a half complete spin crossover (T1/2 =250 K), which was detected by variable temperature crystallography as well. On the other hand, solvated complex 3⋅C3 H6 O exhibited permanent high spin state behaviour and either recrystallization or in situ thermal desolvation converts 3⋅C3 H6 O to solvent-free and spin-crossover-active form 3. Magnetic properties of all the reported complexes were also supported by EPR spectroscopy experiments and in addition, DFT and ab initio calculations were employed for the evaluation of the g-factor and zero field splitting parameters.

Quantum Crystallography: Current Developments and Future Perspectives.

Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.

NO Releasing and Anticancer Properties of Octahedral Ruthenium-Nitrosyl Complexes with Equatorial 1 H-Indazole Ligands.

With the aim of enhancing the biological activity of ruthenium-nitrosyl complexes, new compounds with four equatorially bound indazole ligands, namely, trans-[RuCl(Hind)4(NO)]Cl2·H2O ([3]Cl2·H2O) and trans-[RuOH(Hind)4(NO)]Cl2·H2O ([4]Cl2·H2O), have been prepared from trans-[Ru(NO2)2(Hind)4] ([2]). When the pH-dependent solution behavior of [3]Cl2·H2O and [4]Cl2·H2O was studied, two new complexes with two deprotonated indazole ligands were isolated, namely [RuCl(ind)2(Hind)2(NO)] ([5]) and [RuOH(ind)2(Hind)2(NO)] ([6]). All prepared compounds were comprehensively characterized by spectroscopic (IR, UV-vis, 1H NMR) techniques. Compound [2], as well as [3]Cl2·2(CH3)2CO, [4]Cl2·2(CH3)2CO, and [5]·0.8CH2Cl2, the latter three obtained by recrystallization of the first isolated compounds (hydrates or anhydrous species) from acetone and dichloromethane, respectively, were studied by X-ray diffraction methods. The photoinduced release of NO in [3]Cl2 and [4]Cl2 was investigated by cyclic voltammetry and resulting paramagnetic NO species were detected by EPR spectroscopy. The quantum yields of NO release were calculated and found to be low (3-6%), which could be explained by NO dissociation and recombination dynamics, assessed by femtosecond pump-probe spectroscopy. The geometry and electronic parameters of Ru species formed upon NO release were identified by DFT calculations. The complexes [3]Cl2 and [4]Cl2 showed considerable antiproliferative activity in human cancer cell lines with IC50 values in low micromolar or submicromolar concentration range and are suitable for further development as potential anticancer drugs. p53-dependence of Ru-NO complexes [3]Cl2 and [4]Cl2 was studied and p53-independent mode of action was confirmed. The effects of NO release on the cytotoxicity of the complexes with or without light irradiation were investigated using NO scavenger carboxy-PTIO.

Detection of simple inorganic and organic molecules over Cu-decorated circumcoronene: a combined DFT and QTAIM study.

Nowadays graphene materials have attracted a considerable attention because of their potential utilization as gas sensors, biosensors, or adsorbents. Doping or decorating the graphene surface with transition metals can significantly tune its electronic properties and chemical reactivity. Circumcoronene, being a polyaromatic hydrocarbon composed of 19 benzene rings, can be used as a model system of a tiny graphene quantum dot. The adsorption of a set of small molecules (water, hydrogen peroxide, methanol, ethanol, and oxygen) over the copper-decorated circumcoronene was theoretically investigated using density functional theory (DFT) and Bader's quantum theory of atoms in molecules (QTAIM). Following the obtained B3LYP energies, the adsorption of O2 and the chemisorption of H2O2 were found to be energetically the most favorable, with energetic outcomes of -3.6 eV and -3.7 eV, respectively. Moreover, an H2O2 molecule was decomposed during the chemisorption on the Cu atom to form a neutral Cu(OH)2 molecule. Changes in the electronic structure of the studied systems, in particular the oxidation of copper, after the adsorption were investigated within the framework of QTAIM (e.g., charges, bond critical points, and delocalization indices) and partial density of states (PDOS) analysis. The results of this study suggest the suitability of the Cu-decorated graphene materials as adsorbents and/or gas sensors in practical applications.

Ligand Substituent Effects in Manganese Pyridinophane Complexes: Implications for Oxygen-Evolving Catalysis.

A series of Mn(II) complexes of differently substituted pyridinophane ligands, (Py2NR2)MnCl2 (R = iPr, Cy) and [(Py2NR2)MnF2](PF6) (R = iPr, Cy, tBu) are synthesized and characterized. The electrochemical properties of these complexes are investigated by cyclic voltammetry, along with those of previously reported (Py2NMe2)MnCl2 and the Mn(III) complex [(Py2NMe2)MnF2](PF6). The electronic structure of this and other Mn(III) complexes is probed experimentally and theoretically, via high-frequency and -field electron paramagnetic resonance (HFEPR) spectroscopy ab initio quantum chemical theory (QCT), respectively. These studies show that the complexes contain relatively typical six-coordinate Mn(III). The catalytic activity of these complexes toward both H2O2 disproportionation and H2O oxidation has also been investigated. The rate of H2O2 disproportionation decreases with increasing substituent size. Some of these complexes are active for electrocatalytic H2O oxidation; however this activity cannot be rationalized in terms of simple electronic or steric effects.

Spectroscopic and Computational Studies of Spin States of Iron(IV) Nitrido and Imido Complexes.

High-oxidation-state metal complexes with multiply bonded ligands are of great interest for both their reactivity as well as their fundamental bonding properties. This paper reports a combined spectroscopic and theoretical investigation into the effect of the apical multiply bonded ligand on the spin-state preferences of threefold symmetric iron(IV) complexes with tris(carbene) donor ligands. Specifically, singlet (S = 0) nitrido [{PhB(ImR)3}FeN], R = tBu (1), Mes (mesityl, 2) and the related triplet (S = 1) imido complexes, [{PhB(ImR)3}Fe(NR')]+, R = Mes, R' = 1-adamantyl (3), tBu (4), were investigated by electronic absorption and Mössbauer effect spectroscopies. For comparison, two other Fe(IV) nitrido complexes, [(TIMENAr)FeN]+ (TIMENAr = tris[2-(3-aryl-imidazol-2-ylidene)ethyl]amine; Ar = Xyl (xylyl), Mes), were investigated by 57Fe Mössbauer spectroscopy, including applied-field measurements. The paramagnetic imido complexes 3 and 4 were also studied by magnetic susceptibility measurements (for 3) and paramagnetic resonance spectroscopy: high-frequency and -field electron paramagnetic resonance (for 3 and 4) and frequency-domain Fourier-transform (FD-FT) terahertz electron paramagnetic resonance (for 3), which reveal their zero-field splitting parameters. Experimentally correlated theoretical studies comprising ligand-field theory and quantum chemical theory, the latter including both density functional theory and ab initio methods, reveal the key role played by the Fe 3dz2 (a1) orbital in these systems: the nature of its interaction with the nitrido or imido ligand dictates the spin-state preference of the complex. The ability to tune the spin state through the energy and nature of a single orbital has general relevance to the factors controlling spin states in complexes with applicability as single molecule devices.

HFEPR and Computational Studies on the Electronic Structure of a High-Spin Oxidoiron(IV) Complex in Solution.

Nonheme iron enzymes perform diverse and important functions in biochemistry. The active form of these enzymes comprises the ferryl, oxidoiron(IV), [FeO](2+) unit. In enzymes, this unit is in the high-spin, quintet, S = 2, ground state, while many synthetic model compounds exist in the spin triplet, S = 1, ground state. Recently, however, Que and co-workers reported an oxidoiron(IV) complex with a quintet ground state, [FeO(TMG3tren)](OTf)2, where TMG3tren = 1,1,1-tris{2-[N2-(1,1,3,3-tetramethylguanidino)]ethyl}amine and OTf = CF3SO3(-). The trigonal geometry imposed by this ligand, as opposed to the tetragonal geometry of earlier model complexes, favors the high-spin ground state. Although [FeO(TMG3tren)](2+) has been earlier probed by magnetic circular dichroism (MCD) and Mössbauer spectroscopies, the technique of high-frequency and -field electron paramagnetic resonance (HFEPR) is superior for describing the electronic structure of the iron(IV) center because of its ability to establish directly the spin-Hamiltonian parameters of high-spin metal centers with high precision. Herein we describe HFEPR studies on [FeO(TMG3tren)](OTf)2 generated in situ and confirm the S = 2 ground state with the following parameters: D = +4.940(5) cm(-1), E = 0.000(5), B4(0) = -14(1) × 10(-4) cm(-1), g⊥ = 2.006(2), and g∥ = 2.03(2). Extraction of a fourth-order spin-Hamiltonian parameter is unusual for HFEPR and impossible by other techniques. These experimental results are combined with state-of-the-art computational studies along with previous structural and spectroscopic results to provide a complete picture of the electronic structure of this biomimetic complex. Specifically, the calculations reproduce well the spin-Hamiltonian parameters of the complex, provide a satisfying geometrical picture of the S = 2 oxidoiron(IV) moiety, and demonstrate that the TMG3tren is an "innocent" ligand.

Importance of Relativistic Effects and Electron Correlation in Structure Factors and Electron Density of Diphenyl Mercury and Triphenyl Bismuth.

This study investigates the possibility of detecting relativistic effects and electron correlation in single-crystal X-ray diffraction experiments using the examples of diphenyl mercury (HgPh2) and triphenyl bismuth (BiPh3). In detail, the importance of electron correlation (ECORR), relativistic effects (REL) [distinguishing between total, scalar and spin-orbit (SO) coupling relativistic effects] and picture change error (PCE) on the theoretical electron density, its topology and its Laplacian using infinite order two component (IOTC) wave functions is discussed. This is to develop an understanding of the order of magnitude and shape of these different effects as they manifest in the electron density. Subsequently, the same effects are considered for the theoretical structure factors. It becomes clear that SO and PCE are negligible, but ECORR and scalar REL are important in low- and medium-order reflections on absolute and relative scales-not in the high-order region. As a further step, Hirshfeld atom refinement (HAR) and subsequent X-ray constrained wavefunction (XCW) fitting have been performed for the compound HgPh2 with various relativistic and nonrelativistic wave functions against the experimental structure factors. IOTC calculations of theoretical structure factors and relativistic HAR as well as relativistic XCW fitting are presented for the first time, accounting for both scalar and spin-orbit relativistic effects.

Charge and Spin States in Schiff Base Metal Complexes with a Disiloxane Unit Exhibiting a Strong Noninnocent Ligand Character: Synthesis, Structure, Spectroelectrochemistry, and Theoretical Calculations.

Mononuclear nickel(II), copper(II), and manganese(III) complexes with a noninnocent tetradentate Schiff base ligand containing a disiloxane unit were prepared in situ by reaction of 3,5-di-tert-butyl-2-hydroxybenzaldehyde with 1,3-bis(3-aminopropyl)tetramethyldisiloxane followed by addition of the appropriate metal(II) salt. The ligand H2L resulting from these reactions is a 2:1 condensation product of 3,5-di-tert-butyl-2-hydroxybenzaldehyde with 1,3-bis(3-aminopropyl)tetramethyldisiloxane. The resulting metal complexes, NiL·0.5CH2Cl2, CuL·1.5H2O, and MnL(OAc)·0.15H2O, were characterized by elemental analysis, spectroscopic methods (IR, UV-vis, X-band EPR, HFEPR, (1)H NMR), ESI mass spectrometry, and single crystal X-ray diffraction. Taking into account the well-known strong stabilizing effects of tert-butyl groups in positions 3 and 5 of the aromatic ring on phenoxyl radicals, we studied the one-electron and two-electron oxidation of the compounds using both experimental (chiefly spectroelectrochemistry) and computational (DFT) techniques. The calculated spin-density distribution and localized orbitals analysis revealed the oxidation locus and the effect of the electrochemical electron transfer on the molecular structure of the complexes, while time-dependent DFT calculations helped to explain the absorption spectra of the electrochemically generated species. Hyperfine coupling constants, g-tensors, and zero-field splitting parameters have been calculated at the DFT level of theory. Finally, the CASSCF approach has been employed to theoretically explore the zero-field splitting of the S = 2 MnL(OAc) complex for comparison purposes with the DFT and experimental HFEPR results. It is found that the D parameter sign strongly depends on the metal coordination geometry.

Ab initio X(1)0(+) ground state potential curves of Pb···RG dimers (RG = He, Ne, Ar) including spin-orbit effects. Simulation of diffusion coefficients.

CCSD(T) ground state potential curves of Pb···RG systems (RG = He, Ne and Ar) are presented and the importance of the inclusion of spin-orbit effects is discussed. The closed-shell character of the Pb atom at the two-component relativistic level of relativistic theory leads to shallower potential energy curves compared to scalar relativistic open-shell calculations. The pressure-independent cross-diffusion coefficients pD12 have been simulated using the extrapolated two-component CCSD(T) ground state potential curves. The diffusion coefficients from scattering theory are compared with simulations based on molecular dynamics (MD) using the velocity autocorrelation function (VACF) and the Einstein equation. A correction for the proper assessment of the uncertainty in the VACF is proposed. The acceleration of the MD simulation of Pb in RG diffusion is proposed utilizing the RG in Pb diffusion. The dU[TQ]Z/CCSD(T) potential curve of Pb···He (De = 8.667 cm(-1), re = 4.683 Å) supports only one vibrational level. The anharmonicity of this potential is compared to the potential of He···He which also supports only one vibrational level. The comparison is based on the mean square separations of the vibrational wave function.

Conformational, spectroscopic, and molecular dynamics DFT study of precursors for new potential antibacterial fluoroquinolone drugs.

Biological activity, functionality, and synthesis of (fluoro)quinolones is closely related to their precursors (for instance 3-fluoroanilinoethylene derivatives) (i.e., their functional groups, conformational behavior, and/or electronic structure). Herein, the theoretical study of 3-fluoroanilinoethylene derivatives is presented. Impact of substituents (acetyl, methyl ester, and ethyl ester) on the conformational analysis and the spectral behavior is investigated. The B3LYP/6-311++G** computational protocol is utilized. It is found that the intramolecular hydrogen bond N-H···O is responsible for the energetic preference of anti (a) conformer (anti position of 3-fluoroanilino group with respect to the C═C double bond). The Boltzmann ratios of the conformers are related to the differences of the particular dipole moments and/or their dependence on the solvent polarity. The studied acetyl, ethyl ester, and methyl ester substituted fluoroquinolone precursors prefer in the solvent either EZa, ZZa, or both conformers equally, respectively. In order to understand the degree of freedom of rotation of the trans ethyl ester group, B3LYP/6-311G** molecular dynamic simulations were carried out. Vibrational frequencies, electron transitions, as well as NMR spectra are analyzed with respect to conformational analysis, including the effect of the substituent. X-ray structures of the precursors are presented and compared with the results of the conformational analysis.