Formation of carnosine - an ab initio study

Formation of carnosine from histidine and b-alanine is studied by ab initio MO-LCAO-SCF method followed by the perturbative configuration interaction (MP2) in vacuo. After the full geometry optimization at the SCF level, the molecular properties were evaluated and followed by the vibrational-rotational analysis. Consequently, the energy, entropy and free energy were evaluated for the reactants and products of the reaction histidine + beta-alanine = carnosine + H2O and finally the equilibrium constant was enumerated.

Distinctive Supramolecular Features of β-Cyclodextrin Inclusion Complexes with Antidepressants Protriptyline and Maprotiline: A Comprehensive Structural Investigation

Depression, a global mental illness, is worsened due to the coronavirus disease 2019 (COVID-2019) pandemic. Tricyclic antidepressants (TCAs) are efficacious for the treatment of depression, even though they have more side effects. Cyclodextrins (CDs) are powerful encapsulating agents for improving molecular stability, water solubility, and lessening the undesired effects of drugs. Because the atomic-level understanding of the β-CD–TCA inclusion complexes remains elusive, we carried out a comprehensive structural study via single-crystal X-ray diffraction and density functional theory (DFT) full-geometry optimization. Here, we focus on two complexes lining on the opposite side of the β-CD–TCA stability spectrum based on binding constants (Kas) in solution, β-CD–protriptyline (PRT) 1—most stable and β-CD–maprotiline (MPL) and 2—least stable. X-ray crystallography unveiled that in the β-CD cavity, the PRT B-ring and MPL A-ring are aligned at a nearly perfect right angle against the O4 plane and primarily maintained in position by intermolecular C–H···π interactions. The increased rigidity of the tricyclic cores is arising from the PRT -CH=CH- bridge widens, and the MPL -CH2–CH2- flexure narrows the butterfly angles, facilitating the deepest and shallower insertions of PRT B-ring (1) and MPL A-ring (2) in the distorted round β-CD cavity for better complexation. This is indicated by the DFT-derived complex stabilization energies (ΔEstbs), although the complex stability orders based on Kas and ΔEstbs are different. The dispersion and the basis set superposition error (BSSE) corrections were considered to improve the DFT results. Plus, the distinctive 3D arrangements of 1 and 2 are discussed. This work provides the first crystallographic evidence of PRT and MPL stabilized in the β-CD cavity, suggesting the potential application of CDs for efficient drug delivery.

ß-Cyclodextrin Inclusion Complexes with Catechol-Containing Antioxidants Protocatechuic Aldehyde and Protocatechuic Acid—An Atomistic Perspective on Structural and Thermodynamic Stabilities

Protocatechuic aldehyde (PCAL) and protocatechuic acid (PCAC) are catechol derivatives and have broad therapeutic effects associated with their antiradical activity. Their pharmacological and physicochemical properties have been improved via the cyclodextrin (CD) encapsulation. Because the characteristics of b-CD inclusion complexes with PCAL (1) and PCAC (2) are still equivocal, we get to the bottom of the inclusion complexation by an integrated study of single-crystal X-ray diffraction and DFT full-geometry optimization. X-ray analysis unveiled that PCAL and PCAC are nearly totally shielded in the b-CD wall. Their aromatic rings are vertically aligned in the b-CD cavity such that the functional groups on the opposite side of the ring (3,4-di(OH) and 1-CHO/1-COOH groups) are placed nearby the O6–H and O2–H/O3–H rims, respectively. The preferred inclusion modes in 1 and 2 help to establish crystal contacts of OH×××O H-bonds with the adjacent b-CD OH groups and water molecules. By contrast, the DFT-optimized structures of both complexes in the gas phase are thermodynamically stable via the four newly formed host–guest OH⋯O H-bonds. The intermolecular OH×××O H-bonds between PCAL/PCAC 3,4-di(OH) and b-CD O6–H groups, and the shielding of OH groups in the b-CD wall help to stabilize these antioxidants in the b-CD cavity, as observed in our earlier studies. Moreover, PCAL and PCAC in distinct lattice environments are compared for insights into their structural flexibility.

Theoretical Investigation of the Size Effect on the Oxygen Adsorption Energy of Coinage Metal Nanoparticles

This study evaluates the finite size effect on the oxygen adsorption energy of coinage metal (Cu, Ag and Au) cuboctahedral nanoparticles in the size range of 13 to 1415 atoms (0.7–3.5 nm in diameter). Trends in particle size effects are well described with single point calculations, in which the metal atoms are frozen in their bulk position and the oxygen atom is added in a location determined from periodic surface calculations. This is shown explicitly for Cu nanoparticles, for which full geometry optimization only leads to a constant offset between relaxed and unrelaxed adsorption energies that is independent of particle size. With increasing cluster size, the adsorption energy converges systematically to the limit of the (211) extended surface. The 55-atomic cluster is an outlier for all of the coinage metals and all three materials show similar behavior with respect to particle size. Graphic Abstract

Structural, Vibrational and UV/Vis Studies of Adamantane-Containing Triazole Thiones by Spectral, DFT and Multi-reference ab initio Methods

The Fourier transform infrared and Raman spectra of two adamantane-containing triazole thiones, namely 3-(adamantan-1-yl)-1-[(4-benzylpiperazin-1-yl)methyl]-4-phenyl-1H-1,2,4-triazole-5(4H)-thione and 3-(adamantan-1-yl)-4-phenyl-1-[(4-phenylpiperazin-1-yl)methyl]-1H-1,2,4-triazole-5(4H)-thione, were examined in the ranges of 3200–650 cm−1 and 3200–150 cm−1, respectively. The density functional theory calculations were performed for the geometric structures and vibrational spectra for the title molecules. The accurate equilibrium geometry structures of the molecules were determined on the basis of full geometry optimization at the B3LYP/cc-pVDZ level of the theory. The IR and Raman vibrational spectra were calculated and compared with the experimental ones. The experimental vibrational FT-IR and Raman spectra were interpreted. Based on the structure of the molecules the biological activity indices were predicted. It is established that compounds under consideration are very likely to exhibit the analgesic activities. The UV/Vis spectra of solution of the compounds in ethanol were measured in the range of 450–200 nm. The UV/Vis spectra simulations at the Time-Dependent DFT and Multi-Reference Perturbation Theory levels of theory demonstrate unsuitability of the TDDFT for description of the experimental spectra of the title molecules. It is highly probable that this is a consequence of the intramolecular charge transfer. In contrast, the MRPT results are in a good agreement with the experimental spectra.

Density Functional Theory Calculation of Molecular Descriptors for Simple Coumarins in Gas and Different Solvents

The primary aim of this study is to show the importance of molecular structure analysis of pharmaceutical active coumarins compounds using quantum chemistry methods based on density functional theory. To explore the theoretical calculations for global descriptors, the standard Gaussian 09W program was used for coumarins compounds. The full geometry optimization was carried out by the B3LYP/6-311G level of theory. The octanol-water and air-water partition coefficients were also estimated using functional density theory. The order of the HOMO-LUMO energy gap for studied coumarins in the gas phase is umbelliferone (UBA) < (herniarin) HNR ~ (crenulatin) CNT < (scopoletin) SCT < (scoparone) SCO < (isoscopoletin) IST < (4-methylesculetin) MST < (umbelliferone-2- carboxylic acid) UCA < (isofraxidin) IFD < (fraxetin) FXT < (aesculetine) ACT < (dapnetine) DPT. Therefore, UBA molecule in gas phase is less stable. Compared to the measured index of electrophilicity (DE). The MST molecule is stronger, more reactive, nucleophile electrophile at the gas phase and in solvents. In all solvent phases, CNT and UCA molecules have lower values, which mean they are strong nucleophiles. From the log P values of ACT and MST coumarins are in between 1.35-1.8, so ACT and MST coumarins use oral and intestinal absorptions.

A CFD Based Application of Support Vector Regression to Determine the Optimum Smooth Twist for Wind Turbine Blades

Computational fluid dynamics (CFD) is a powerful tool to estimate accurately the aerodynamic loads on wind turbine blades at the expense of high requirements like the duration of computation. Such requirements grow in the case of blade shape optimization in which several analyses are needed. A fast and reliable way to mimic the CFD solutions is to use surrogate models. In this study, a machine learning technique, the support vector regression (SVR) method based on a set of CFD solutions, is used as the surrogate model. CFD solutions are calculated by solving the Reynolds-averaged Navier–Stokes equation with the k-epsilon turbulence model using a commercial solver. The support vector regression model is then trained to give a functional relationship between the spanwise twist distribution and the generated torque. The smooth twist distribution is defined using a three-node cubic spline with four parameters in total. The optimum twist is determined for two baseline blade cases: the National Renewable Energy Laboratory (NREL) Phase II and Phase VI rotor blades. In the optimization process, extremum points that give the maximum torque are easily determined since the SVR gives an analytical model. Results show that it is possible to increase the torque generated by the NREL VI blade more than 10% just by redistributing the spanwise twist without carrying out a full geometry optimization of the blade shape with many shape-defining parameters. The increase in torque for the NREL II case is much higher.

Electronic structure and bonding analysis of transition metal sandwich and half-sandwich complexes of the triphenylene ligand

Full geometry optimization using the BP86 and B3LYP methods has been carried out for all of the low-energy isomers of half-sandwich L3M(Tphn) (Tphn = triphenylene, M = Ti–Ni, and L3 = (CO)3, Cp–) and sandwich M(Tphn)2 (Tphn = triphenylene and M = Ti, Cr, Fe, Ni) structures. Depending on the electron richness of the molecule and the nature of the metal, a complete rationalization of the bonding in triphenylene complexes has been provided. The triphenylene adopts various hapticities from η2 to η6, some of them involving full or partial coordination of the C6 ring and shown to be quite flexible with respect to the ground spin state. The triphenylene behavior remains dependent on the electron-withdrawing and electron-donor properties of the (CO)3M and CpM fragments, respectively. For the sandwich complexes, both triphenylene ligands prefer to behave differently depending on the coordination mode to satisfy the metal electron demand.

Substitution effects and electronic properties of the azo dye (1-phenylazo-2-naphthol) species: a TD-DFT electronic spectra investigation

DFT/B3LYP and ab initio Hartree–Fock calculations with full geometry optimization have been carried out on hydrazo and azo forms of 1-phenylazo-2-naphthol and their substituted derivatives. The predicted geometries show that a small energy difference of 1.8 kcal/mol might tune the equilibrium between both forms. Depending on the electron donating and electron accepting of the different used substituents (CF3, NH2, CH3, Cl, and NO2), the various obtained isomers show small energy differencies between meta and para substitution except for the NH2 one, indicating the coexistence of the tautomers in solution. The ortho(C12) position was found to be the less favored substitution in all cases, while the second ortho(C16) position for different substituents provides isomers competing with the most stable meta and para ones. The obtained results suggest that a judicious choice in the substituents’ use on the phenyl ring should lead to stabilization. The TD-DFT theoretical study performed on the optimized geometry allowed us to identify quite clearly the spectral position and the nature of the different electronic transitions according to their molecular orbital localization, hence, reproducing the available UV-Vis spectra. The increase in the wavelength values is in perfect agreement with red shifts and the ΔE (ELUMO – EHOMO) decreasing. Thus, from the point of view of both substitution and the used solvent, the obtained electronic spectra appear to behave quite differently.

Microwave Assisted Synthesis, Antifungal Activity, and DFT Study of Some Novel Triazolinone Derivatives

A series of some novel 1,2,4-triazol-5(4H)-one derivatives were designed and synthesized under microwave irradiation via multistep reaction. The structures of 1,2,4-triazoles were confirmed by1H NMR, MS, FTIR, and elemental analysis. The antifungal activities of 1,2,4-triazoles were determined. The antifungal activity results indicated that the compounds5c,5f, and5hexhibited good activity againstPythium ultimum, and the compounds5band5cdisplayed good activity againstCorynespora cassiicola. Theoretical calculation of the compound5cwas carried out with B3LYP/6-31G (d). The full geometry optimization was carried out using 6-31G(d) basis set, and the frontier orbital energy and electrostatic potential were discussed, and the structure-activity relationship was also studied.