Vibrational Stark Fields in Carboxylic Acid Dimers

Carboxylic acids form exceptionally stable dimers and have been used to model proton and double proton transfer processes. The stabilization energies of the carboxylic acid dimers are very weakly dependent on the nature of the substitution. However, the electric field experienced by the OH group of a particular carboxylic acid is dependent more on the nature of the substitution on the dimer partner. In general, the electric field was higher when the partner was substituted with electron-donating group and lower with electron-withdrawing substituent on the partner. The Stark tuning rate (∆μ) of the O–H stretching vibrations calculated at the MP2/aug-cc-pVDZ level was found to be weakly dependent on the nature of substitution on the carboxylic acid. The average Stark tuning rate of O–H stretching vibrations of a particular carboxylic acid when paired with other acids was 5.7 cm–1 (MV cm–1)–1, while the corresponding average Stark tuning rate of the partner acids due to a particular carboxylic acid was 21.9 cm–1 (MV cm–1)–1. The difference in the Stark tuning rate is attributed to the primary and secondary effects of substitution on the carboxylic acid. The average Stark tuning rate for the anharmonic O–D frequency shifts is about 40-50% higher than the corresponding harmonic O–D frequency shifts calculated at B3LYP/aug-cc-pVDZ level, much greater than the typical scaling factors used, indicating the strong anharmonicity of O–H/O–D oscillators in carboxylic acid dimers. Finally, the linear correlation observed between pKa and the electric field was used to estimate the pKa of fluoroformic acid to be around 0.9.

Thermodynamic properties of single crystals based on lithium tungstate by reaction and DSC calorimetry

For the first time, single crystals of undoped lithium tungstate and lithium tungstate doped by 1.25% molybdenum were grown by the low-temperature-gradient Czochralski technique. The standard formation enthalpies, lattices enthalpies, stabilization energies, and the heat capacity were determined in the temperature range of 320-997 K. The lattice enthalpy dependence on Mo content was constructed.

X-ray Single Crystal Structure, Tautomerism Aspect, DFT, NBO, and Hirshfeld Surface Analysis of a New Schiff Bases Based on 4-Amino-5-Indol-2-yl-1,2,4-Triazole-3-Thione Hybrid

Four different new Schiff basses tethered indolyl-triazole-3-thione hybrid were designed and synthesized. X-ray single crystal structure, tautomerism, DFT, NBO and Hirshfeld analysis were explored. X-ray crystallographic investigations with the aid of Hirshfeld calculations were used to analyze the molecular packing of the studied systems. The H···H, H···C, S···H, Br···C, O···H, C···C and N···H interactions are the most important in the molecular packing of 3. In case of 4, the S···H, N···H, S···C and C···C contacts are the most significant. The results obtained from the DFT calculations indicated that the thione tautomer is energetically lower than the thiol one by 13.9545 and 13.7464 kcal/mol for 3 and 4, respectively. Hence, the thione tautomer is the most stable one which agree with the reported X-ray structure. In addition, DFT calculations were used to compute the electronic properties while natural bond orbital calculations were used to predict the stabilization energies due to conjugation effects. Both compounds are polar where 4 (3.348 Debye) has a higher dipole moment than 3 (2.430 Debye).

A Computational Study of the Conformational Behavior of 2,5-Dimethyl- 1,4-dithiane-2,5-diol and Analogous S and Se: DFT and NBO Study

Conformational behaviors of 2,5-dimethyl-1,4-dithiane-2,5-diol (compound 1), 2,5- dimethyl-1,4-dithiane-2,5-dithiol (compound 2) and 2,5-dimethyl-1,4-dithiane-2,5-diselenol (compound 3) were investigated by the B3LYP/6-311+G **, the M06-2X/aug-ccpvdz levels of theory and natural bond orbital NBO analysis. The structures and the structural parameters of the mentioned molecules were optimized by the B3LYP and the M06-2X methods. We assessed the roles and contributions of the effective factors in the conformational properties of the mentioned compounds by means of the B3LYP and M06-2X levels of theory and the NBO interpretations. The stereoelectronic effects of the mentioned molecules were studied using the NBO analysis. The results showed that the stereoelectronic effects were in favor of the (ax,ax) conformers (the most stable conformations), from compound 1 to compound 3; therefore, these effects have impacts on the conformational properties of compounds 1-3, and stabilization energies associated with LP2X→ σ*S1-C2 electron delocalization, where [X= O, S, and Se], for 1-ax, ax conformer has the greatest value between all of the other conformers. Therefore, according to the calculated thermodynamic parameters, the stability of the 1-ax, ax compound was justified by the presence of LP2X→σ*S1-C2 electron delocalization. A molecular orbital explanation was conducted to investigate the correlations between the linear combinations of natural bond orbitals in the HOMOs, LUMOs and the molecular reactivity parameters. There is a direct relationship between the stereoelectronic effects, molecular reactivity and thermodynamic parameters of compounds 1 to 3 as the harder ax, ax conformations with the greater stereoelectronic effects and ΔG(eq-ax) values are more stable than their corresponding eq, eq conformers. Besides frontier molecular orbitals (FMOs), mapped molecular electrostatic potential (MEP) surfaces of conformations of compounds 1 to 3 were investigated.

Interaction Analyses on SARS-CoV-2 Spike Protein Based on Large-Scale Correlated Fragment Molecular Orbital Calculations

At the stage of SARS-CoV-2 infection to human cell, the spike protein consisting of three chains, A, B and C, with a total of 3.3 thousand residues plays the key role, and thus its nature have attracted considerable interests. Here, we report interaction analyses on the spike protein of both closed (PDB-ID: 6VXX) and open (6VYB) structures, based on large-scale fragment molecular orbital (FMO) calculations at the level of up to the fourth-order Møller-Plesset perturbation with singles, doubles and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. By two separate calculations for the RBD complexes with angiotensin converting enzyme 2 (ACE2) (6M0J) and B38 Fab antibody (7BZ5), it was found that this stabilization loss of RBD was partially compensated by the binding with ACE2 or antibody.

Interaction Analyses on SARS-CoV-2 Spike Protein Based on Large-Scale Correlated Fragment Molecular Orbital Calculations

At the stage of SARS-CoV-2 infection to human cell, the spike protein consisting of three chains, A, B and C, with a total of 3.3 thousand residues plays the key role, and thus its nature have attracted considerable interests. Here, we report interaction analyses on the spike protein of both closed (PDB-ID: 6VXX) and open (6VYB) structures, based on large-scale fragment molecular orbital (FMO) calculations at the level of up to the fourth-order Møller-Plesset perturbation with singles, doubles and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. By two separate calculations for the RBD complexes with angiotensin converting enzyme 2 (ACE2) (6M0J) and B38 Fab antibody (7BZ5), it was found that this stabilization loss of RBD was partially compensated by the binding with ACE2 or antibody.

[(Z)-N-(3-Fluorophenyl)-O-methylthiocarbamato-κS](triphenylphosphane-κP)gold(I): crystal structure, Hirshfeld surface analysis and computational study

The title phosphanegold(I) thiolate, C26H22AuFNOPS or [Au(C8H7FNOS)(C18H15P)], has the AuI centre coordinated by phosphane-P [2.2494 (8) Å] and thiolate-S [2.3007 (8) Å] atoms to define a close to linear geometry [P—Au—S = 176.10 (3)°]. The thiolate ligand is orientated so that the methoxy-O atom is directed towards the Au atom, forming an Au...O close contact of 2.986 (2) Å. In the crystal, a variety of intermolecular contacts are discerned with fluorobenzene-C—H...O(methoxy) and phenyl-C—H...F interactions leading to dimeric aggregates. These are assembled into a three-dimensional architecture by phenyl-C—H...S(thiolate) and phenyl-C—H...π(fluorobenzene, phenyl) interactions. Accordingly, the analysis of the calculated Hirshfeld surface shows 30.8% of all contacts are of the type C...H/H...C but this is less than the H...H contacts, at 44.9%. Other significant contributions to the surface come from H...F/F...H [8.1%], H...S/S...H [6.9%] and H...O/O...H [3.2%] contacts. Two major stabilization energies have contributions from the phenyl-C—H...π(fluorobenzene) and fluorobenzene-C—H...C(imine) interactions (−37.2 kcal mol−1), and from the fluorobenzene-C—H...F and phenyl-C—H...O interactions (−34.9 kcal mol−1), the latter leading to the dimeric aggregate.