Structural flexibility of favipiravir and its structural analogues in solutions: experimental and computational insight.

Combined UV-vis and quantum chemical studies of the structural flexibility and tautomerism of 6-R-3-hydroxy-2-pyrazine carboxamides in solutions revealed that their keto-enol transformations are accompanied by the deprotonation of enol tautomers and the formation of the corresponding anionic species. Both the solvent and the 6-R substituent strongly influence the relative abundance of the above forms in solutions. Anions are not formed in 1,2-dichloroethane (DCE), but the probability of deprotonation in neutral water and N,N-dimethylformamide (DMF) increases in the order R = H < F < NO2. Only enol tautomers of all solutes are found in DCE. DMF stabilizes keto forms only moderately and assists much strongly in the deprotonation of all three compounds. Water tends to stabilize both keto tautomers and deprotonated anions: the keto form dominates in the case of R = H (antiviral drug T-1105), the anions are found exclusively for R = NO2, and the aqueous solution of another antiviral drug, favipiravir (R = F), contains both the keto tautomer and the anionic form. The results of quantum chemical free energy calculations are in agreement with the experimental observations.

Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine.

As in the case of cytosine [Phys. Chem. Chem. Phys. 2023, 25, 24121-24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine-d2 have been computationally reproduced and interpreted with the use of the recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions [J. Phys. Chem. B, 2020, 124, 6664-6670]. A cluster model of a solute surrounded by 30 water molecules is shown to be sufficient to reproduce experimental vibrational frequencies and relative Raman intensities with the use of B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ simulations. Analogous PBE-D3 computations provided a less good, but still reasonably accurate, modeling of Raman spectra. It is shown that strong changes of frequencies and relative intensities of the Raman bands of thymine, caused by its hydration, can be interpreted mainly as a result of hydrogen bonding with 6 nearest water molecules. Non-negligible improvement of the quality of simulations for larger clusters comprising water molecules that do not have direct contacts with the solute, suggests that spectroscopic effects of hydration should be ascribed to the joined action of solute-solvent and solvent-solvent interactions. Nevertheless, the moderate number of water molecules required for successful simulations of the Raman spectra of aqueous thymine, suggests that the vibrational modes and derivatives of the polarizability of the solute are mainly locally influenced, while the effect of bulk water is rather modest.

Computational analysis of the vibrational spectra and structure of aqueous cytosine.

The recently developed efficient protocol for the explicit quantum mechanical modeling of the structure and IR spectra of liquids and solutions [Katsyuba et al., J. Phys. Chem. B, 2020, 124, 6664-6670] is used to describe aqueous solutions of cytosine. The same cluster model of a solute surrounded by the first solvation shell of solvent molecules was shown to be sufficient to reproduce experimental vibrational frequencies and relative IR and Raman intensities. An equally good quality of Raman spectra was provided by B3LYP-D3/def2-TZVP and B3LYP-D3/aug-cc-pVDZ simulations. Computations using the PBE functional were sufficient for modeling of the IR spectra but failed in the simulations of Raman scattering. It is shown that strong changes of frequencies and relative intensities of Raman and IR bands of cytosine, caused by its hydration, cannot be completely assigned to the influence of hydrogen bonds (HBs) with 7 or 8 closest water molecules. They are rather ascribed to the combined effect of solute-solute and solute-solvent HBs with the participation of at least 30 water molecules separating cytosine from the bulk solvent. This suggests that the vibrational modes and derivatives of the polarizability and dipole moment of the solute are mainly locally influenced by its first hydration shell, while the influence of bulk water is rather modest.

Supramolecular Optimization of Sensory Function of a Hemicurcuminoid through Its Incorporation into Phospholipid and Polymeric Polydiacetylenic Vesicles: Experimental and Computational Insight.

This work presents the synthesis of a new representative of hemicurcuminoids with a nonyloxy substituent (HCur) as a fluorescent amphiphilic structural element of vesicular aggregates based on phosphatidylcholine (PC), phosphatidylserine (PS), and 10,12-pentacosadiynoic acid (PCDA). Both X-ray diffraction analysis of the single crystal and 1H NMR spectra of HCur in organic solvents indicate the predominance of the enol-tautomer of HCur. DFT calculations show the predominance of the enol tautomer HCur in supramolecular assemblies with PC, PS, and PCDA molecules. The results of the molecular modeling show that HCur molecules are surrounded by PC and PS with a rather weak exposure to water molecules, while an exposure of HCur molecules to water is enhanced under its supramolecular assembly with PCDA molecules. This is in good agreement with the higher loading of HCur into PC(PS) vesicles compared to PCDA vesicles converted into polydiacetylene (PDA) ones by photopolymerization. HCur molecules incorporated into HCur-PDA vesicles exhibit greater planarity distortion and hydration effect in comparison with HCur-PC(PS) ones. HCur-PDA is presented as a dual fluorescence-chromatic nanosensor responsive to a change in pH within 7.5-9.5, heavy metal ions and polylysine, and the concentration-dependent fluorescent response is more sensitive than the chromatic one. Thus, the fluorescent response of HCur-PDA allows for the distinguishing between Cd2+ and Pb2+ ions in the concentration range 0-0.01 mM, while the chromatic response allows for the selective sensing of Pb2+ over Cd2+ ions at their concentrations above 0.03 mM.

Thermodynamics of trans/gauche conformational equilibria and vibrational spectra of 1,2-dihaloethanes in various media.

The recently developed efficient protocols to implicit [Grimme et al., J. Phys. Chem. A 125, 4039-4054 (2021)] and explicit quantum mechanical modeling of non-rigid molecules in solution [Katsyuba et al., J. Phys. Chem. B 124, 6664-6670 (2020)] are used to describe conformational equilibria of 1,2-dichloroethane and 1,2-dibromoethane in various media. Two approaches for evaluation of trans/gauche free energy differences, ΔGt-g, are compared: (a) direct ΔGt-g computation in implicit solution; (b) the use, together with experimental intensities, of infrared absorption coefficients and Raman scattering cross sections computed for each explicitly modeled solution. The same cluster model of a solute surrounded by the first solvation shell of solvent molecules was used to simulate both Raman and IR spectra. The good agreement between the two approaches indicates the reliability of both methods. The importance of using correct absorption coefficients and Raman scattering factors for each medium is discussed. The ΔGt-g estimates from both implicit and explicit solvation simulations were combined with experimentally measured enthalpy differences ΔHt-g available in the literature to obtain condensed-state ΔSt-g estimates.

Deep-Blue Emissive Copper(I) Complexes Based on P-Thiophenylethyl-Substituted Cyclic Bisphosphines Displaying Photoinduced Structural Transformations of the Excited States.

A synthetic method for a primary 2-(thiophen-2'-yl)ethylphosphine was developed. The reaction of thiophenylethylphosphine with paraformaldehyde and primary arylamines leads to the formation of cyclic bisphosphines, namely, 1,5-di(aryl)-3,7-bis(thiophenylethyl)-1,5-diaza-3,7-diphosphacyclooctane (aryl = phenyl, p-tolyl). The obtained bisphosphines form cationic bis-P,P-chelate complexes with copper(I) tetrafluoroborate, which were structurally characterized by NMR spectroscopy, mass spectrometry, and elemental and XRD analyses. Surprisingly, the copper(I) complexes display a multiband emission in the solid state with maxima at 355-360, 425-430, and 480-490 nm and nanosecond lifetimes (1.2-1.4 ns) upon a 335 nm excitation. The excitation of the complexes at 360 nm at room temperature results in a deep-blue emission at 425-430 nm and a tail at 460-490 nm. A temperature decrease leads to an increased intensity of the emission band at 480 nm, while the luminescence lifetimes insignificantly increased up to 14 ns. Quantum chemical calculations explain the observed unusual luminescent behavior by the existence of "undistorted" and "flattened" singlet excited states of copper(I) complexes at room temperature and at 77 K, respectively.

What quantum chemical simulations tell us about the infrared spectra, structure and interionic interactions of a bulk ionic liquid.

The recently developed efficient protocol to explicit quantum mechanical modeling of the structure and IR spectra of liquids and solutions [Katsyuba et al., J. Phys. Chem. B, 2020, 124, 6664-6670] is applied to ionic liquid 1-ethyl-3-methyl-imidazolium tetrafluoroborate [Emim][BF4], and its C2-deuterated analog [Emim-d][BF4]. It is shown that the solvation strongly modifies the frequencies and IR intensities of both cationic and anionic components of the ionic liquids. The main features of the bulk spectra are reproduced by the simulations for cluster ([Emim][BF4])8, representing an ion pair solvated by the first solvation shell. The geometry of the cluster closely resembles the solid-state structure of the actual ionic liquid and is characterized by short contacts of all CH moieties of the imidazolium ring with [BF4]- anions. Both structural and spectroscopic analyses allow the contacts to be interpreted as hydrogen bonds of approximately equal strength. The enthalpies of these liquid-state H-bonds, estimated with the use of empirical correlations, amount to 1.2-1.5 kcal mol-1, while the analogous estimates obtained for the gas-phase charged species [Emim][BF4]2- and [Emim]2[BF4]+ increase to 3.6-3.9 kcal mol-1.

Computer-aided simulation of infrared spectra of ethanol conformations in gas, liquid and in CCl4 solution.

The recently developed efficient protocol combining implicit and explicit, accurate quantum-mechanical modeling of the condensed state (Katsyuba et al., J. Chem. Phys. 155, 024507 [2021]) is used to describe the IR spectra of liquid ethanol and its solutions in CCl4 . The relative abundance of the anti and gauche conformers of ethanol is shown to increase from ~40:60 in the gas phase to ~55:45 in the liquid phase. In spite of a moderate impact of media effects on the conformational composition of the liquid, the solvent strongly influences vibrational frequencies, IR intensities, and normal modes of each conformer, producing qualitatively different spectra compared to the gas phase and CCl4 solution. Further, these solvent effects affecting IR frequencies and intensities depend not only on the conformation of the solvated molecule but also on the solvating species. Nevertheless, vibrational frequencies of anti and gauche conformers of liquid ethanol and its several isotopomers practically coincide with each other. Convenient liquid-state conformational markers in the fingerprint region of IR spectra are revealed for the hydroxyl-deuterated species: CH3 CH2 OD, CH3 CHDOD, CH3 CD2 OD, and CD3 CD2 OD.

Revisiting conformations of methyl lactate in water and methanol.

The recently developed efficient protocols to implicit [Grimme et al., J. Phys. Chem. A 125, 4039-4054 (2021)] and explicit quantum mechanical modeling of non-rigid molecules in solution [Katsyuba et al., J. Phys. Chem. B 124, 6664-6670 (2020)] are applied to methyl lactate (ML). Building upon this work, a new combination scheme is proposed to incorporate solvation effects for the computation of infrared (IR) absorption spectra. Herein, Boltzmann populations calculated for implicitly solvated single conformers are used to weight the IR spectra of explicitly solvated clusters with a size of typically ten solvent molecules, i.e., accounting for the first solvation shell. It is found that in water and methanol, the most abundant conformers of ML are structurally modified relative to the gas phase, where the major form is ML1, in which the syn conformation of the -OH moiety is stabilized by a OH⋯O=C intramolecular hydrogen bond (HB). In solution, this syn conformation transforms to the gauche form because the intramolecular HB is disrupted by explicit water molecules that form intermolecular HBs with the hydroxyl and carbonyl groups. Similar changes induced by the gas-solution transition are observed for the minor conformers, ML2 and/or ML3, characterized by OH⋯OCH3 intramolecular HB in the gas phase. The relative abundance of ML1 is shown to decrease from ∼96% in gas to ∼51% in water and ∼92% in methanol. The solvent strongly influences frequencies, IR intensities, and normal modes, resulting in qualitatively different spectra compared to the gas phase. Some liquid-state conformational markers in the fingerprint region of IR spectra are revealed.

Synthesis, structure, and electrochemical properties of 4,5-diaryl-1,2,3-triphosphaferrocenes and the first example of multi(phosphaferrocene).

The reaction between aryl substituted sodium 1,2,3-triphospholides or disodium bis(1,2,3-triphospholide) and [Fe(η6-(C6H5CH3)Cp]+[PF6]- in boiling diglyme results in pure 1,2,3-triphosphaferrocenes 1-3 or bis(1,2,3-triphosphaferrocene) 4, respectively, in good yields. The structure of all obtained 1,2,3-triphosphaferrocenes 1-4 has been extensively studied experimentally (NMR, UV-Vis spectroscopy, and X-ray analysis for 1 and 4) and quantum chemically. The electrochemical properties of 1,2,3-triphosphaferrocenes 1-4 in the solid state were studied for the first time and a reversible one-electron oxidation (E1/2 = 0.52-0.92 V vs. Fc+/Fc) was demonstrated for 1, 3, and 4. In the case of 1,4-bis(5-phenyl-4-(1,2,3-triphospaferrocenyl))benzene 4, consecutive oxidation in the solid state is observed in contrast to other 1,2,3-triphosphaferrocenes 1-3. According to the ESR data, the g-factor of the oxidized bis(1,2,3-triphosphaferrocene), 4 (g = 2.12) is different from the g-factors of oxidized 1,2,3-triphosphaferrocenes 1-3 (g = 2.01). This is the first example of multi(ferrocenyl) systems based on the phosphaferrocene motif, which in turn opens up a new fundamental platform for the preparation of compounds with stimuli-responsive properties.

Triple-bridged helical binuclear copper(i) complexes: Head-to-head and head-to-tail isomerism and the solid-state luminescence.

A family of helical dinuclear copper(i) pyridylphospholane complexes [Cu2L3X]X (X = BF4-, Cl- and Br-) was prepared. The family includes the first examples of this type of complex based on copper(i) chloride and copper(i) bromide. The two isomers typical of this class of compounds, namely head-to-head and head-to-tail complexes, were studied in solution by spectroscopic and optical methods, and in the solid state by X-ray diffraction. Furthermore, the solid-state luminescence of the complexes at different temperatures was studied, and the results were interpreted using quantum-chemical calculations. It was shown that the luminescence of the complexes is attributed to the 3(M + X)LCT transitions.

Fast and Accurate Quantum Chemical Modeling of Infrared Spectra of Condensed-Phase Systems.

An efficient approach for an accurate quantum mechanical (QM) modeling of infrared (IR) spectra of condensed-phase systems is described. An ensemble of energetically low-lying cluster structures of a solute molecule surrounded by an explicit shell of solvent molecules is efficiently generated at the semiempirical tight-binding QM level and then reoptimized at the density functional theory level of theory. The IR spectrum of the solvated molecule is obtained as a thermodynamic average of harmonically computed QM spectra for all significantly populated cluster structures. The accuracy of such simulations in comparison to experimental data for some organic compounds and their solutions is shown to be the same or even better than the corresponding QM computations of the gas-phase IR spectrum for the isolated molecule.

Acid-Catalyzed Rearrangements of 3-Aryloxirane-2-Carboxamides: Novel DFT Mechanistic Insights.

Efficient synthesis of 3-arylquinolin-2(1H)-ones and N-(2-carboxyaryl)-oxalamides from protic acid-catalyzed rearrangements of 3-aryloxirane-2-carboxamides was achieved recently but not well understood. In contrast to the classical Meinwald rearrangement, extensive DFT calculations reveal that the proximal aryl and amide groups have strong synergetic effects to control the amide-aided and aryl-directed oxirane-opening and further rearrangement sequences. The ortho-nitro substituent of the proximal aryl is directly involved in a nucleophilic oxirane ring-opening, the amide C=O is an important proton shuttle for facile H-shifts, while the N-aryl may act as a potential ring-closing site via Friedel-Crafts alkylation. The mechanistic insights are useful for rational design of novel synthesis by changing the aryl and amide functional groups proximal to the oxirane ring.

Characterization of Conjugation Effects in the Series of Quinoxaline-2-ones by Means of Vibrational Raman Spectroscopy.

A broad series of quinoxalinone-based π-conjugated donor-acceptor fluoro- and NLO-phores is characterized by means of Raman spectroscopy and single-crystal X-ray analysis supported by quantum chemical computations. Intense Raman spectroscopic markers that allow the differentiation of even closely related structures are identified. The intensities of these bands are shown to be related to the conjugation of the different molecular moieties, and they can provide an estimation of its extent. The intensity redistribution between these markers serves as a source of auxiliary structural information capable of pointing to a distortion of the conjugation or to the influence of aggregation effects in the condensed state. A simple relation between the intensity of the marker and the position and oscillator strength of the lowest-energy electronic absorption band of quinoxalinones allows a linking of the Raman effect with the optical properties of these compounds, which can be used for the rational design of novel species with improved optical characteristics.

One-Electron Reduction of Acenaphthene-1,2-Diimine Nickel(II) Complexes.

New nickel-based complexes of 1,2-bis[(2,6-diisopropylphenyl)imino]acenaphthene (dpp-bian) with BF4 - counterion or halide co-ligands were synthesized in THF and MeCN. The nickel(I) complexes were obtained by using two approaches: 1) electrochemical reduction of the corresponding nickel(II) precursors; and 2) a chemical comproportionation reaction. The structural features and redox properties of these complexes were investigated by using single-crystal X-ray diffraction (XRD), cyclic voltammetry (CV), and electron paramagnetic resonance (EPR) and UV/Vis spectroscopy. The influence of temperature and solvent on the structure of the nickel(I) complexes was studied in detail, and an uncommon reversible solvent-induced monomer/dimer transformation was observed. In the case of the fluoride complex, the unpaired electron was found to be localized on the dpp-bian ligand, whereas all of the other nickel complexes contained neutral dpp-bian moieties.

2,3-(Dibenzimidazol-2-yl)quinoxalines: Unexpected Dynamical Effect on Steady-State Electronic Absorption Spectra.

We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ solutions cannot be assigned to electronic excitations of the equilibrium ground-state DBIQ structure. Extended consideration including the nonequilibrium structures within the framework of ab initio molecular dynamics (MD) revealed the importance of torsion molecular motions not covered by the static case. The strong impact of solute-solvent hydrogen bonding on stabilization of these nonequilibrium structures and on conformational composition of DBIQ was demonstrated. A presence of twisted nonplanar geometries along the whole MD trajectory was shown to drastically influence not only energies but also characters of electronic excitations, resulting in a change of local π-π* character in a solution of 1,2-dichloroethane to charge-transfer character in polar dimethylsulfoxide.

Intriguing Near-Infrared Solid-State Luminescence of Binuclear Silver(I) Complexes Based on Pyridylphospholane Scaffolds.

A series of novel charged disilver(I) complexes with pyridyl-containing phospholanes was synthesized. These complexes were characterized using a range of spectroscopic techniques and single-crystal and powder X-ray diffraction. The complexes demonstrate solid-state near-infrared (NIR) luminescence (765-902 nm) that is unique for dinuclear AgI complexes. Combined spectroscopic/quantum chemical analysis suggests that the NIR luminescence of complexes 4-6 in the solid state is mainly due to crystal packing effects.

Fast Quantum Chemical Simulations of Infrared Spectra of Organic Compounds with the B97-3c Composite Method.

The ability of the quantum chemical computations to reproduce spectral positions and relative intensities of infrared (IR) bands for experimental vibrational spectra of organic molecules is assessed. The efficient B97-3c density functional approximation, routinely applicable to hundreds of atoms on a single processor, has been applied for the simulation of IR spectra for species containing up to 216 atoms. The results demonstrate that B97-3c, being much faster than the well-recognized hybrid functional B3LYP, offers similarly good quantitative performance in comparison to experimental data for relative IR intensities and fundamental frequencies (ν ≤ 2200 cm-1) for isolated molecules comprising from 3 to 21 first- or second-row atoms.

The Assembly of Unique Hexanuclear Copper(I) Complexes with Effective White Luminescence.

The unique L2Cu6I6 complexes containing two Cu3I3 units have been obtained via reaction of 1,5-diaza-3,7-diphosphacyclooctanes bearing ethylpyridyl substituents at phosphorus atoms with an excess of copper iodide. The structure of one of the complexes was confirmed by X-ray diffraction. It was shown that the complexes can exist in two crystalline phases with different parameters of the unit cell, which were detected by the PXRD data analyses. The solvent-free crystalline phases of the complexes display rare solid-state white emission at room temperature, which is observed due to the presence of two broad bands in the emission spectra with maxima at 464 and 610 nm. Quantum chemical computations show that the high-energy band has 3(M+X)LCT origin, whereas the low-energy band is interpreted as 3CC. The quantum yields of white luminescence of complexes reach 15-20%.

Leaching from Palladium Nanoparticles in an Ionic Liquid Leads to the Formation of Ionic Monometallic Species.

Molecular dynamics simulations and DFT calculations suggest that leaching of palladium species from Pd nanoparticles in ionic liquids does not involve "naked" Pd(0) atoms or neutral ArPdX species formed by oxidative addition of arylhalides. Instead, the ionic liquid contributes largely to leaching of ionic PdX- or PdAr+ species.