A Quantum Chemical Study on the Relative Stability of Diaminodinitroethylene Isomers

We report an in-depth theoretical study of 4-styrylpyridine in its singlet S(0) ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree-Fock (HF), second-order Møller-Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post-HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis=trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car-Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within approximately 1 ps during the simulation carried out at 150 K on this isomer.

The distinctive properties of cadmium selenide (CdSe) semiconductor situated it in a multitudinous number of applications. Although (CdSe)2 cluster has more than one isomer, the previous studies concentrated merely on one isomer. The goal of this study was to determine the various stable geometric structure isomers of (CdSe)2 clusters; also, structural, electronic, and optical properties of the stable isomers are investigated using density functional theory (DFT). First, geometry optimization calculations of the possible geometric isomers were carried out using the BroydenFletcher-Goldfarb-Shanno minimization (BFGS) algorithm. Total ground-state energy calculations showed that all the converged isomers have a high probability of existing in any experiment, relying on the implemented experimental technique. Twenty initial possible geometric structures were investigated, in which eleven isomers were converged. However, all of them are relaxed in the 2D planar geometry. The results showed that eleven possible stable isomers were disclosed, where the final structures of the converged isomers produced six different structures; three of them were not detected before. The rhombus structure was ascertained to be the most stable isomer followed by the trapezoidal structure of (CdSe)2. The isomers’ Cd-Se bond length are 2.50-2.74 A, and the average Cd-Se-Cd, Se-Cd-Se angles were 64.5o-123o and 56.3o-114.2o, respectively. Furthermore, the bond angles show that the selenium atom lone-pairs electrons are responsible for shifting the isomers’ structure from the linearity. The total ground-state energy differences were 0.00-1.82 eV. The calculated highest occupied molecular orbital (HOMO), and the lowest unoccupied molecular orbital (LUMO) gap of the isomers implied that the gap depends on the symmetrical geometry of the isomer. Furthermore, it was evident that the most stable isomers are accompanied with larger gaps. The HOMO-LUMO graphs demonstrated that HOMO orbitals were localized around the selenium atom, while LUMO orbitals were distributed around both cadmium and selenium atoms. The calculated absorption spectrum was unique for each isomer. The absorption edges for the isomers are ranging from 2.53 to 3.73 eV. The results show that the obtained absorption spectra peaks’ values (nm) are smaller compared to CdSe experimental results. (CdSe)2 clusters are very active that they straightforwardly react to produce larger clusters. Finally, the results of this study corroborate with previous computational studies.

Pharmacophore Oriented MP2 Characterization of Charge Distribution for Anti-SARS-CoV-2 Inhibitor Nirmatrelvir

The trans–cis and the azide–tetrazole ring-chain isomerization of 2-azido-1,3-azoles: Quantum chemical study

Molecular hydrogen is considered an ideal next-generation energy carrier. There are two methods of hydrogen molecule adsorption: chemical adsorption and physical adsorption. Since chemical adsorption is strong and physical adsorption is weak, an intermediate adsorption mode is necessary to achieve reversible adsorption and desorption at room temperature. In this study, quantum chemical calculations were used to investigate a solid-phase manganese hydrogen complex, [Mn(CO)(dppe)2-H2]+ (referred to as Mn1, and dppe = 1,2-bis(diphenylphosphino)ethane), to determine whether reversible adsorption and desorption at temperature relatively close to room temperature is feasible. Furthermore, since the adsorption energy for D2 is not the same as that for H2, the feasibility of separating D2 and H2 was explored by Gibbs energy calculations at different temperatures using the density functional theory. Based on adsorption measurements conducted at 310-365 K, the D2/H2 separation factor for Mn1 ranged from 2 to 1.5 as observed in our previous study. The results calculated using the M06-2X functional indicated that the D2/H2 separation factor for Mn1 at 298 K was approximately 2.55, which is superior to the results obtained using the B3LYP and CAM-B3LYP functionals. The isotope separation ability of [Mn(CO)3(PCy3)2-H2]+ (referred to as Mn2) is slightly inferior to that of Mn1; however, it has an advantage of lower adsorption enthalpy compared to Mn1, making it more suitable for desorption at lower temperatures.

The adsorption of cis and trans 2-butenes on Pt(111) has been studied as a function of hydrogen coverage θH by means of calculations based on density functional theory (DFT) with the inclusion of dispersion forces. All hydrogen coverages have been considered, from 0 to 1.00 monolayer (ML). For each case, the di-σ and π adsorption geometries of the olefins have been compared at a surface coverage of θC4H8 = 0.11 ML. Calculations of the Gibbs free energies of these systems have identified the most stable 2-butene isomer (cis or trans) as a function of coverage, temperature, and pressure. In particular, focus was placed on two sets of conditions, namely, one with a pressure of 10–7 Torr, a temperature of 80 K, and a gas ratio (PH2/Pbutene) of 25, similar to the conditions used in surface-science studies, and a second with a pressure of 1 bar, a temperature range of 300–400 K, and a gas ratio (PH2/Pbutene) of 10, similar to catalytic hydrogenation conditions. With all selected functionals (PW91, PBE-TS, and optPBE), di-σ bonding was found to be the most stable for both isomers of 2-butene and for all hydrogen coverages except for θH = 1.00 ML. At low pressures, 2-butene is physisorbed at low temperatures (≤125 K with PBE-TS and ≤90 K with optPBE); however, when the temperature increases, coadsorption of the butene with 6 H atoms becomes the most stable configuration of the system (θH = 0.67 ML), and finally, 2-butene desorbs around 380 K, as estimated with PBE-TS (or around 325 K with optPBE). Interestingly, a switch in stability was observed with hydrogen coverage, from the adsorbed trans isomer being the more stable for θH < 0.44 ML to the adsorbed cis isomer becoming the more stable at higher hydrogen coverages, in agreement with the cis–trans isomerization behavior previously reported for this system. At high pressures, the behavior is similar, but with transitions occurring at higher temperatures. 2-Butene is physisorbed until the temperature reaches 250 K, and desorbs above 500 K. At hydrogenation reaction temperatures (between 300 and 500 K), a hydrogen coverage of roughly half a monolayer was calculated (0.66 and 0.44 for 300 and 500 K, respectively). Our results confirm that dispersion effects must be included to properly describe the 2-butene and hydrogen coadsorption on Pt(111), as PW91 predicts that 2-butene is never adsorbed on the platinum surface. On the other hand, DFT calculations including dispersion forces such as PBE-TS or optPBE afford a good understanding of catalytic systems under both ultra-high-vacuum conditions and catalytic hydrogenation conditions. For this system, the PBE-TS results are in good agreement with experiments: they correctly reproduce the coverage in hydrogen and the configuration of the 2-butene adsorbate (cis–trans isomer).

Molecular structure of formanilide is determined by gas-phase electron diffraction (GED) augmented by quantum chemical calculations (B3LYP/cc-pVTZ and MP2/cc-pVTZ) and literature microwave (MW) data. The combined GED and MW data are well reproduced for the mixture of trans and cis isomers with the relative abundance of 59 ± 5 and 41 ± 5 %, respectively, at T = 410 K. The trans isomer (C s symmetry) is planar, while the cis isomer (C 1 symmetry) has the twisted structure with the amide group rotated by 36.7 ± 2.7° with respect to the phenyl ring. In accord with theoretical calculations, the amide bond –NH–C(O)– is planar in trans formanilide and a somewhat nonplanar in cis isomer. Accurate structural parameters were obtained by a simultaneous fit of the rotational constants reported in the literature and GED intensities obtained in this study. The N–C(O) and N–CPh bond dissociation energies in formanilide are calculated using Gaussian-4 method. It is revealed that the strength of N–C(O) bond in formanilide is 50 kJ/mol less than that in benzamide. On the contrary, the strength of adjacent bond (N–CPh) increases by 35 kJ/mol compared to aniline. It is rather unexpectedly that the bond strength weakening does not result in the bond elongating, and vice versa.

Synthesis, spectral and theoretical (DFT) investigations of 4,6-diphenyl-6-hydroxy-1-{[(1Z)-1-phenyl ethylidene] amino}tetrahydropyrimidine-2(1H)-one

Time-dependent density functional theory has been used to calculate nonlinear optical (NLO) properties, including the first and second hyperpolarizabilities as well as the two-photon absorption cross-section, for the donor-acceptor molecules p-nitroaniline and dimethylamino nitrostilbene, and for respective materials attached to a gold dimer. The CAMB3LYP, B3LYP, PBE0, and PBE exchange-correlation functionals all had fair but variable performance when compared to higher-level theory and to experiment. The CAMB3LYP functional had the best performance on these compounds of the functionals tested. However, our comprehensive analysis has shown that quantitative prediction of hyperpolarizabilities is still a challenge, hampered by inadequate functionals, basis sets, and solvation models, requiring further experimental characterization. Attachment of the Au2S group to molecules already known for their relatively large NLO properties was found to further enhance the response. While our calculations show a modest enhancement for the first hyperpolarizability, the enhancement of the second hyperpolarizability is predicted to be more than an order of magnitude.

The use of photosensitizers as organic ligands in metal–organic frameworks (MOFs) is a common practice to engineer their UV/vis optical absorption. For instance, MOFs consisting of porphyrin ligands usually inherit their light-harvesting properties and thus follow the Gouterman model in which the low-lying excitations correspond to π → π* transitions. However, the characterization of the excited states of porphyrin ligands in MOFs requires an appropriate description of the periodic crystal including the metal nodes and intermolecular interactions. Here, we investigate the UV/vis absorption properties of porphyrin-MOF Al-PMOF, its two metalated forms, Zn-Al-PMOF and Co-Al-PMOF, and their corresponding isolated porphyrin ligands using density functional theory (DFT)/time-dependent DFT (TDDFT) simulations with Perdew–Burke–Ernzerhof (PBE), PBE0, and CAM-B3LYP functionals. Our results indicate that hybrid functionals are necessary to capture the proper nature of the transitions and the excitonic effects of the optical and fundamental gaps in porphyrin molecules and porphyrin-MOFs that the PBE functional fails to describe. Likewise, the simulations show that a wrong representation of some excitations can be obtained depending on the functional and when the Tamm–Dancoff approximation is used. Finally, our results show that the PBE and PBE0 functionals are not able to capture the gap renormalization when going from the isolated molecules to the periodic crystals. Overall, the nature of the optical transitions, excitonic effects, and gap renormalization are important features to assess in the prediction of optical properties in MOF crystals that require considering proper functionals and approximations to overcome the main failures of DFT/TDDFT calculations.

Deferiprone and other 3-hydroxy-4-pyridinones are used in metal chelation therapy of iron overload. To investigate the structure and stability of these compounds in the natural aqueous environment, ferric complexes of deferiprone and amino acid maltol conjugates were synthesized and studied by computational and optical spectroscopic methods. The complexation caused characteristic intensity changes, a 300× overall enhancement of the Raman spectrum, and minor changes in UV-vis absorption. The spectra were interpreted on the basis of density functional theory (DFT) calculations. The CAM-B3LYP and ωB97XD functionals with CPCM solvent model were found to be the most suitable for simulations of the UV-vis spectra, whereas B3LYP, B3LYPD, B3PW91, M05-2X, M06, LC-BLYP, ωB97XD, and CAM-B3LYP functionals were all useful for simulation of the Raman scattering. Characteristic Raman band frequencies for 3-hydroxy-4-pyridinones were assigned to molecular vibrations. The computed conformer energies consistently suggest the presence of another isomer of the deferiprone-ferric complex in solution, in addition to that found previously by X-ray crystallography. However, the UV-vis and Raman spectra of the two species are similar and could not be resolved. In comparison to UV-vis, the Raman spectra and their combination with calculations appear more promising for future studies of iron sequestrating drugs and artificial metalloproteins as they are more sensitive to structural details.

The 2-nitro-2'-hydroxy-5'-methylazobenzene molecule is characterized by an intramolecular hydrogen bond of the N...OH type. The parameters of this bond were calculated within density functional theory (DFT) and the continuum solvation model (cpcm) in the gas phase and individual protic and aprotic solvents: hexane, toluene, dimethylformamide, diethylamine, 2-propanol and water at 298.15 K. B3LYP, cam-B3LYP and D3B3LYP functionals and 6-311++g (d, p) basis set was used. The most energetically favorable form of existence of the 2-nitro-2'-hydroxy-5'-methylazobenzene molecule should be considered its cis-isomer, which forms an intramolecular hydrogen bond of the proton of the hydroxy group with the β-nitrogen atom of the –N=N– group. Such conformer is more coplanar both in the gas phase and in solution. The intramolecular hydrogen bond should be classified as moderately strong with a significant contribution of electrostatic component. The binding energy is in the range of 33 to 51 kJ/mol, the O-H...N flat angle is 138-143°, and the length does not exceed 1.7-1.8 Å. An increase in the dielectric constant of the solvent and its solvating ability leads to a weakening of the binding energy, but its length is no changed almost. Theoretical study of prototropic equilibrium showed that the activation barriers to proton transfer in the gas phase and solutions do not exceed 20 kJ/mol. However, the calculation of ΔG0298 and experimental UV spectra of 2-nitro-2’-hydroxy-5’-methylazobenzene in solutions of various compositions proves that a quinoid structure is not formed in any of the solvents studied. A comparison of the calculation results and spectroscopy data allows us to conclude that the cam-B3LYP functional, which takes into account the correction for dispersion interactions, most correctly describes the structure of the 2-nitro-2'-hydroxy-5'-methylazobenzene molecule in solution. For citation: Fedorova A.A., Lefedova O.V. On intramolecular hydrogen bond in the molecule of 2-nitro-2’-hydroxy-5’-methylazobenzene. ChemChemTech [Izv. Vyssh. Uchebn. Zaved. Khim. Khim. Tekhnol.]. 2025. V. 68. N 7. P. 74-84. DOI: 10.6060/ivkkt.20256807.7212.

Various hybrid functionals (B3LYP, B97-2, PBE0, BMK, BH&HLYP, CAM-B3LYP, and LC-ωPBE) implemented in density functional theory were applied to give estimate of static first hyperpolarizabilty (β(0)) of (E)-benzaldehyde phenylhydrazone designated as (E)-BPH. Against those of MP2 computations as a function of the underlying density functional, good agreement was obtained with the BH&HLYP and CAM-B3LYP functionals. The LC-ωPBE functional and the B3LYP, PBE0, B97-2, and BMK functionals underestimated and overestimated β(0), respectively. The basis set effect on the calculated β(0) was also investigated. It turned out that the 6-311+G(2d,p) basis set provided excellent converged value of β(0). On the basis of the calculated results, we investigated the substituent effect on β(0) of donor-acceptor (D-A) substituted (E)-BPH systematically by using the BH&HLYP and CAM-B3LYP computations with the 6-311+G(2d,p) basis set. We proposed a Zwitterion structure to explain the calculated trend in the substituent effect and the enhanced hyperpolarizability of type II compounds (A-(E)-BPH-D) than type I compounds (D-(E)-BPH-A). Natural bonding orbital analysis carried out at BH&HLYP/6-311+G(2d,p)//B3LYP/6-31G(2df,p) level of theory substantiated the claim.

First-principle computations were carried out on the conformational space of trans and cis peptide bond isomers of HCO-Thr-NH2. Using the concept of multidimensional conformational analysis (MDCA), geometry optimizations were performed at the B3LYP/6-31G(d) level of theory, and single-point energies as well as thermodynamic functions were calculated at the G3MP2B3 level of theory for the corresponding optimized structures. Two backbone Ramachandran-type potential energy surfaces (PESs) were computed, one each for the cis and trans isomers, keeping the side chain at the fully extended orientation (chi1=chi2=anti). Similarly, two side chain PESs for the cis and trans isomers were generated for the (phi=psi=anti) orientation corresponding to approximately the betaL backbone conformation. Besides correlating the relative Gibbs free energy of the various stable conformations with the number of stabilizing hydrogen bonds, the process of trans-->cis isomerization is discussed in terms of intrinsic stabilities as measured by the computed thermodynamic functions.

The paper compares the experimental FT-IR, UV-vis, and 1H NMR spectra of isoconazole and bifonazole with the density functional theory (DFT) calculations using different functionals. The results were compared with previously reported data related to their analogue, posaconazole. The analysis of calculated IR spectra with use of CAM-B3LYP (isoconazole) or B3LYP (bifonazole) functionals shows good accordance with the experimental IR spectrum. The best compatibility between the experimental and theoretical UV spectra was observed with the use of B3LYP or wB97XD functionals for isoconazole or bifonazole, respectively. The reason for the difference in the UV-vis spectra of isoconazole and bifonazole was discussed based on linear response time-dependent DFT and natural bond orbital methods. The calculated 1H NMR spectrum shows that the DFT formalism, particularly the B3LYP functional, give an accurate description of the isoconazole and bifonazole chemical shifts.