Structural Chemistry

The development of compounds that selectively modulate thyroid hormone action by serving as subtype-selective ligands of the thyroid hormone receptors (TRs) would be useful for clinical therapy. In the present work, quantitative structure-activity relationship (QSAR) models by adopting molecular descriptors to predict the TR binding activity were established based on a data set of TR ligands. The linear (multiple linear regression (MLR) and partial least squares regression (PLSR)) and nonlinear (support vector machine regression (SVR)) methods were employed to investigate the relationship between structural properties and binding activities. The proposed PLSR model was slightly superior to the MLR model and SVR model, as indicated by the reasonable statistical properties (TRβ: Rtr2 = 0.9594, Qte2 = 0.8091. TRα: Rtr2 = 0.9705, Qte2 = 0.8057). Additionally, molecular docking simulations were also performed to study the probable binding modes of the ligands and the TR subtype selectivity. The results indicate that substituents located in region A, region B, and region C and the orientation of these groups might result in the subtype selectivity based on the hydrogen bonding and electrostatic interactions. The derived QSAR models together with the molecular docking results have good potential in facilitating the discovery of novel TR ligands with improved activity and subtype selectivity.

Quantum mechanical calculations are carried out on the reactions of CH3OCHCl2 (DCDME) with Cl atom by means of DFT and couple cluster methods. The geometries of the reactants, products, and transition states involved in the reaction pathways are optimized at BHandHLYP level of theory using 6-311G(d,p) basis set. Transition states are searched on the potential energy surface involved during the reaction channels, and each of the transition states is characterized by the presence of only one imaginary frequency. The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate calculation. Single point energy calculations are performed at CCSD(T) level using the same basis set. The hydrogen abstraction rate constant for the title reaction is calculated at 298 K and atmospheric pressure using the canonical transition state theory including tunneling correction. The calculated value for rate constant as 1.204 × 10−12 cm3 molecule−1 s−1 is found to be in very good agreement with the recent experimental data. The percentage contributions of both reaction channels are also reported at 298 K.

Phản ứng của diethanolamine với diferrocenylmethyl carbonium (2) được tạo ra từ diferrocenylmethanol (1) khi xử lý với BF3 trong CH2Cl2 đã cung cấp tổng hợp hợp chất có tiêu đề diferrocenylmethoxyethylamine (3). Cấu trúc của 3 đã được xác định bằng phương pháp tán xạ tia X (XRD) với dữ liệu tinh thể: nhóm không gian đơn phương P21/n và a=5.8419(14) Å, b=13.572(3) Å, c=23.839(6) Å, α=90°, β=91.827(5)°, γ=90°, V=1889.2(8) Å3, Z=4, Dc=1.558 mg·m−3, μ=1.548 mm−1, F(000)=920. Các chế độ liên kết hydro trong và giữa các phân tử trong 3 đã được chứng minh cả trong cấu trúc tinh thể phân tử và đặc trưng quang phổ IR.

Noncovalent interactions have an impact on the properties of condensed phases, solutions, and crystals. These interactions can occur between groups within a molecule (intra-) or between molecules (inter-). The current report examines a series of molecular balances as a quantitative method for evaluating the electronic effects of electron-donating (ED) and electron-withdrawing (EW) substituents in the para-position. Additionally, the impact on the stabilization of the two isomers (open and closed) and the strength of the intramolecular interactions is discussed in the report. The relative stability of the geometrical isomers, as well as the enthalpy, Gibbs free energy, and entropy for all 24 structures are analyzed. It was noted that the stability of the structures was associated with the substituents and the nature of the conformer. A strong positive correlation was observed between the calculated relative enthalpies and total energies as with R2 = 0.96. The calculated ΔH ranges between − 13.77 and 5.74 kJ mol−1, substitution of ED resulted in ΔH < 0, and the most negative value observed for strong ED  namely N(CH3)2. It is worth noting that substitution of EW resulted in positive values of ΔH except for F. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital are found in the ranges − 5.19 to − 6.78 eV and − 5.58 to − 6.16 eV for open and closed conformers, respectively. The preference for the folded state can be attributed to weak S $$\cdots$$ O chalcogen interactions. The observed relationship between electronic effects and torsional and chalcogen bonding properties offers insights into designing and manipulating molecular systems with specific conformational preferences and noncovalent interactions that may have potential implications in the development of molecular switches, sensors, and materials with tailored properties.

It is frequently said that hydrogen bonds (HBs) are enhanced by ionic interactions and in this article we intend to determine the degree at which this reinforcement happens. Considering our interest in the Guanidine(neutral)/Guanidinium(cation) system and its particular nature, all the possible 1:1 complexes with the Chloride(anion)/Hydrochloric acid(neutral) system have been studied at different levels of computation (B3LYP with 6-31+G* and TZVP basis sets; MP2 with 6-31+G*, 6-311++G** and aug-cc-pVDZ basis sets; CBS-QB3 and G3MP2). The nature of these interactions established in all the systems and, when possible, at all the levels of computation used in this study, has been analyzed using Atoms in Molecules and Natural Bond Orbital methodologies. By examining the interaction energy, the electron density at the bond critical bonds, the atomic energy, the charge transfer, the orbital energy, and the deformation energy we can conclude that HBs are stronger when the ionic interaction is stronger. Thus, both interactions do not work in an independent manner but one reinforces the other to different degrees depending on the nature of the charges present. Several correlations with the interaction energy have been found and a partition of the contributions of both the HB and ionic forces to the total interactions is proposed.

For the first time theoretical evidence for the experimentally hitherto unknown astatine azide, AtN3, the heaviest of all halogen azides, is presented. The structure and the vibrational data of AtN3 were computedab initio at RHF and electron-correlated MP2 levels of theory using a quasirelativistic (MWB) pseudopotential for astatine, where the basis functions for the valences andp electrons consist of the standard double-ζ basis set. For nitrogen a standard 6-31G(d) basis was used. The molecule represents a true minimum (NIMAG=0) at all levels of theory applied and is predicted to exist in a planartrans bentC s structure. Since hybrid functionals, which define the exchange functional as a linear combination of Hartree-Fock, local, and gradient-corrected exchange terms, are known to predict the experimental parameters best, we also computed astatine azide (At-N1-N2-N3) at the B3-LYP level; the results are as follows:d(At-N1)=2.267,d(N1–N2)=1.239,d(N2–N3)=1.146 å; ∠(A1-N1-N2)=111.6‡, ∠(N1-N2-N3)=171.9‡;v 1,=157.4,v 2=366.6,v 3=559.0,v 4=659.6,v 5=1264.7,v 6=2165.1 cm−1 (unscaled). The heat of formation was computed at B3-LYP level to be δH (AtN3)=+80 kcal mol−1.

p-Thioacetatebenzoic acid (H2L) and a combination of N-donor ligand of 4,4′-bipyridine (4,4′-bipy) with metal(II) ions give rise to three 3D supramolecules of general formula [M(HL)2(4,4′-bipy)2(H2O)2] · H2O, M = CoII (1), ZnII (2), NiII (3), which were characterized by crystallographic methods. The crystals are isostructural and belong to the triclinic $$ P\bar{1} $$ space group. The structure can be considered to construct from 1D chains and further linked by hydrogen bonds into the final 3D supramolecular networks. The electrochemical behavior of complexes 1 and 3 were studied by cyclic voltammetry, indicating that the electron transfers in the electrode reaction are irreversible. Meanwhile, complex 2 exhibits significantly red-shifted emission in solid state at room temperature. p-Thioacetatebenzoic acid (H2L) and a combination of N-donor ligand of 4,4′-bipyridine (4,4′-bipy) with metal(II) ions give rise to three 3D supramolecules of general formula [M(HL)2(4,4′-bipy)2(H2O)2] · H2O, M = CoII (1), ZnII (2), NiII (3), which were characterized by crystallographic methods. The structure is constructed from 1D chains and further linked by hydrogen bonds into the final 3D supramolecular network.

In the present paper, we report crystal structures of four types ([A(1)H][A(2)H]Y, [A(1)H]3[A(2)H]Y2, A(1)H[A(2)H···A(2)]Y, and A(1)H[A(1)H···A(2)]Y) of mixed salts containing the sulfate anion (Y = SO42−) and amino acids A, i.e., sarcosine (Sar), dimethylglycine (DMG), betaine (Bet), β-alanine (β-Ala), and l-proline (l-Pro): (β-AlaH)(DMGH)SO4·2H2O (I), (β-AlaH)(BetH)SO4 (II), (β-AlaH)(l-ProH)SO4 (III), (BetH)(l-ProH)SO4 (IV), (SarH)3(l-ProH)(SO4)2 (V), (β-AlaH)(l-ProH···l-Pro)SO4 (VI), and (β-AlaH)(β-AlaH···DMG)SO4 (VII). The O···O distances in dimeric cations (l-ProH···l-Pro) and (β-AlaH···DMG) are 2.450(3) and 2.5295(12) Å in (VI) and (VII), respectively. Crystal structure determinations of (β-AlaH)(BetH)SO4 (II) at 100 K (P21/n), 200 K (Pnma), 250 K (Pnma), and room temperature (Pnma) revealed a structural phase transition in the interval between 100 and 200 K.