Search Results (56)

We report a computational investigation on the reachability of the molecular similarity index (MSI) approach for predicting the relative drug strength of methylcarbamate derivatives. Traditional MSI values have been obtained by calculating the overlap integral of total electron momentum densities between one molecule and another. Furthermore, we have proposed and tested orbital-specific MSI (OS-MSI) values, obtained by doing the same but with electron momentum densities of a selected molecular orbital (MO) such as the highest occupied MO (HOMO) and the lowest unoccupied MO (LUMO). In the calculations, a Boltzmann-weighted electron momentum density estimated by a theoretical probability distribution of rotamers was used, while the solvation effect was considered using the polarizable continuum model. It is shown that the traditional MSI values as well as the OS-MSI values for the HOMO do not have any correlation with experimental relative toxicity of the methylcarbamate derivatives. In contrast, it has been observed and found that the OS-MSI values for the LUMO exhibit a noticeable correlation with the experimental data. The reason behind this observation is discussed in relation to the drug reaction mechanism of the methylcarbamate derivatives. Full article

A series of water-soluble molecules based on 8-isopropyl-2-methyl-5-nitroquinoline and 1,10-phenanthroline core were designed by introducing a π-conjugated bridge, vinyl unit –CH=CH–. We present the selective conversion of methyl groups located on the C2 and C9 positions in the constitution of selected quinoline or 1,10-phenanthroline derivatives, respectively, into vinyl (or styryl) products by applying Perkin condensation. The two groups of ligands differ in the presence of one or two arms. The structure of the molecule ((1E,1′E)-(1,10-phenanthroline-2,9-diyl)bis(ethene-2,1-diyl))bis(benzene-4,1,3-triyl) tetraacetate was determined by single-crystal X-ray diffraction measurements. The X-ray, NMR, and DFT computational studies indicate the influence of rotation (rotamers) on the physical properties of studied styryl molecules. The results show that the styryl molecules with the vinyl unit –CH=CH– exhibit significant static and dynamic hyperpolarizabilities. Quantum chemical calculations using density functional theory and B3LYP/6-311++G(d,p) with Grimme’s dispersion correction approach predict the existence and relative stability of different spatial cis(Z)- and trans(E)-conformers of styryl derivatives of quinoline and 1,10-phenanthroline, which exhibit different electronic distribution and conjugation within the molecular skeleton, dipole moments, and steric interactions, leading to variations in their photophysical behavior and various applications. Our studies indicate that the rotation and isomerization of aryl groups can significantly influence the electronic and optical properties of π-conjugated systems, such as vinyl units (–CH=CH–). The rotation of aryl groups around the single bond that connects them to the vinyl unit can lead to changes in the effective π-conjugation between the aryl group and the rest of the π-conjugated system. The rotation and isomerization of aryl groups in π-conjugated systems significantly impact their electronic and optical properties. These changes can modify the efficiency of π-conjugation, affecting charge transfer processes, absorption properties, light emission, and electrical conductivity. In designing optoelectronic materials, such as organic dyes, organic semiconductors, or electrochromic materials, controlling the rotation and isomerization of aryl groups can be crucial for optimizing their functionality. Full article

Because of the involvement of π-electron cyclic constituents in their side chains, the so-called aromatic residues give rise to a number of strong, narrow, and well-resolved lines spread over the middle wavenumber (1800–600 cm⁻¹) region of the Raman spectra of peptides and proteins. The number of characteristic aromatic markers increases with the structural complexity (Phe → Tyr → Trp), herein referred to as (F_i = 1, …, 6) in Phe, (Y_i = 1, …, 7) in Tyr, and (W_i = 1, …, 8) in Trp. Herein, we undertake an overview of these markers through the analysis of a representative data base gathered from the most structurally simple tripeptides, Gly-Xxx-Gly (where Xxx = Phe, Tyr, Trp). In this framework, off-resonance Raman spectra obtained from the aqueous samples of these tripeptides were jointly used with the structural and vibrational data collected from the density functional theory (DFT) calculations using the M062X hybrid functional and 6-311++G(d,p) atomic basis set. The conformation dependence of aromatic Raman markers was explored upon a representative set of 75 conformers, having five different backbone secondary structures (i.e., β-strand, polyproline-II, helix, classic, and inverse γ-turn), and plausible side chain rotamers. The hydration effects were considered upon using both implicit (polarizable solvent continuum) and explicit (minimal number of 5–7 water molecules) models. Raman spectra were calculated through a multiconformational approach based on the thermal (Boltzmann) average of the spectra arising from all calculated conformers. A subsequent discussion highlights the conformational landscape of conformers and the wavenumber dispersion of aromatic Raman markers. In particular, a new interpretation was proposed for the characteristic Raman doublets arising from Tyr (~850–830 cm⁻¹) and Trp (~1360–1340 cm⁻¹), definitely excluding the previously suggested Fermi-resonance-based assignment of these markers through the consideration of the interactions between the aromatic side chain and its adjacent peptide bonds. Full article

Prototropic conversion (prototropy) for heterocyclic nucleobases was already signaled by Watson and Crick about seventy years ago as one of the reasons for nucleic acids mutations. This isomeric phenomenon has been investigated for neutral derivatives by means of both experimental and theoretical procedures, and their favored tautomers discussed in numerous articles published in the last fifty years. Protonation/deprotonation reactions in the gas phase have also been studied using both quantum-chemical calculations and experimental techniques. Some thermochemical parameters of these processes have been documented. However, prototropy has not always been taken into account in protonation/deprotonation reactions. Most frequently, tautomeric heterocycles have been treated as simple polyfunctional compounds without possible intramolecular protontransfers. Taking into account the lack of data for the complete tautomeric mixtures, quantum-chemical investigations have been undertaken by us about twenty-five years ago for prototropic heterosystems. In this work, the pyrimidine base uracil (U) was chosen. It possesses two identical exo groups (=O/OH) at the 2- and 4-positions, two labile (tautomeric) protons, and five conjugated sites (N1, N3, C5, O7, and O8). Different types of isomerism, prototropy and OH-rotation, were considered for the neutral, protonated, and deprotonated forms. Using quantum-chemical methods, thermochemical stabilities of all possible tautomers-rotamers were examined in vacuo and the potential isomers selected. The selected isomeric mixtures for the neutral and ionic forms were applied for the determination of the thermochemical parameters in the four-step acid/base equilibria: B²⁻ BH⁻ BH₂ BH₃⁺ BH₄²⁺, where BH₂ indicates U. For each step, the microscopic (kinetic) and macroscopic (thermodynamic) acid/base parameters were estimated, and sites of the proton gain and proton loss examined. The similarities and differences between the acid/base equilibria for uracil and other pyrimidine nucleobases were discussed. Full article

The synthetic availability and wide range of biological activity of hydrazides and hydrazones make them attractive subjects for investigation. In this study, we focused on synthesis of 2-methyl-5-nitro-6-phenylnicotinohydrazide-based hydrazones derived from the corresponding substituted aldehydes. The structure of the obtained compounds was studied using NMR spectroscopy and DFT calculations. After repeated recrystallization, all the synthesized compounds remained as mixtures of isomers. As a result of a detailed analysis, we found that the duplication and bifurcation of signals in the ¹H NMR spectra for some atoms is a consequence of the existence of four isomers, namely Z-I, Z-II, E-I and E-II. Duplicate proton signals with a chemical shift difference of 0.1–0.2 ppm and in a ratio of about 2:1 were noticed in the experimental data. By modeling the structures of individual configurations and conformations, Gibbs free energy values were obtained, which allowed us to estimate the approximate content of rotamers for the E-isomer equal to 3:2, which coincided with experimental data. We also tested the antibacterial and antifungal activity of the synthesized compounds. Full article

Bostrycoidin is one of the pigments produced by the Fusarium genus of fungi. On the one hand, it has significant pharmacological importance, while on the other hand, it serves as a presence marker of Fusarium infection in useful grain crops, fruits, and soils. In this regard, the structural and optical properties of the bostrycoidin molecule were studied in the framework of density functional theory (DFT). The most stable geometry as well as higher-energy conformers and tautomers were investigated. The lowest-energy tautomer was found to be about 3 kcal/mol higher in energy than the most stable structure, resulting in relatively low population of this state. The obtained conformational rotamers associated with the rotation of the OMe group possess similar energy. The vibrational spectrum was modeled for the most stable conformer, and the most active peaks in the IR absorbance spectrum were assigned. Moreover, the electronic absorption spectrum was simulated within the time-dependent DFT approach. The obtained theoretical spectrum is in good agreement with the experimental data and the theoretically calculated longest-wavelength transition (HOMO–LUMO) was about 498 nm. Full article

The structure of the title compound (4d), unexpectedly obtained in the reaction between o-phenylenediamine and 2-benzoylcyclohexanone instead of the target 3H-benzo[b][1,4]diazepine derivative 3d, was determined spectroscopically in solution and by a single-crystal X-ray diffraction (XRD) study. It involves two enantiomeric rotamers, called forms D and U, of which the structure was elucidated based on NMR spectra measured and predicted in DFT-GIAO calculations. An averaging of δ_Cs for all tautomeric positions in the benzimidazole part of the 4d hydrate studied in wet (probably slightly acidic) CDCl₃ unambiguously indicates tautomeric exchange in its imidazole unit. An XRD analysis of this material confirms the existence of only one tautomer in the solid phase. The non-covalent interactions forming between molecules of water and benzimidazole derivative are shorter than the sum of van der Waals radii and create an infinite-chain hydrogen bond motif along the b-axis. A possible mechanism for the observed cyclocondensation is also proposed. Full article

The interaction between different types of substituents in dicarbollide ligands and their influence on the stabilization of various rotational conformers (rotamers) of transition metal bis(dicarbollide) complexes [3,3′-M(1,2-C₂B₉H₁₁)₂]⁻ are considered. It has been shown that the formation of intramolecular CH···X hydrogen bonds between dicarbollide ligands is determined by the size of the proton acceptor atom X rather than its electronegativity. Due to the stabilization of rotamers with different dipole moments, intramolecular hydrogen bonds between ligands in transition metal bis(dicarbollide) complexes can have a significant impact on the biological properties of their derivatives. In the presence of external complexing metals, weak intramolecular CH···X hydrogen bonds can be broken to form stronger X—>M donor-acceptor bonds. This process is accompanied by the mutual rotation of dicarbollide ligands and can be used in sensors and molecular switches based on transition metal bis(dicarbollide) complexes. Full article

The controlled formation of mixed-metal bimetallics was realised through use of a fac-[Re(CO)₃(N,N′-bpy-P)Cl] complex bearing an exogenous 2,4,6-trioxa-1,3,5,7-tetramethyl-8-phosphaadamantane donor at the 5-position of the bpy. The introduction of gold, silver, and rhodium with appropriate secondary ligands was readily achieved from established starting materials. Restricted rotation about the C_(bpy)-P bond was observed in several of the bimetallic complexes and correlated with the relative steric bulk of the second metal moiety. Related chemistry with the 6-substituted derivative proved more limited in scope with only the bimetallic Re/Au complex being isolated. Full article

In order to look for the origins of tautomeric preferences in neutral creatinine in vacuo, we examined prototropic conversions for model azoles, namely mono-hydroxy and mono-amino imidazoles, and also for their selected 1-methyl derivatives. All possible isomeric forms of creatinine and model compounds, resulting from intramolecular proton transfer (prototropy), conformational isomerism about –OH, and configurational isomerism about =NH, were studied in the gas phase (model of non-polar environment) by means of quantum-chemical methods. Because the bond-length alternation is a consequence of the resonance phenomenon, it was measured for all DFT-optimized structures by means of the harmonic oscillator model of electron delocalization (HOMED) index. Important HOMED analogies were discussed for investigated azoles and compared with those for previously studied cyclic azines, including pyrimidine nucleic acid bases. The internal effects were taken into account, and the stabilities of the investigated tautomers-rotamers were analyzed. Significant conclusions on the favored factors that can dictate the tautomeric preferences in creatinine were derived. Full article

Boron-doped organic compounds display unique properties as a result of the presence of an empty p orbital on boron and the ability to switch between a trigonal planar and a tetrahedral geometry. In recent years, they have found several applications not only as synthetic reagents, e.g., in the Suzuki–Miyaura reaction, but also as pharmaceuticals and as specialized materials due to their optical and electronic properties. Some boron compounds may exist as atropisomers, and these rotamers may have different properties according to their sense of rotation. Synthetic strategies to separate them and, more recently, to obtain them in an asymmetric manner are becoming popular. In this review, we survey the literature on this emerging field of research. Full article

A series of phosphorus and selenium peri-substituted acenaphthene species with the phosphino group oxidized by O, S, and Se has been isolated and fully characterized, including by single-crystal X-ray diffraction. The P(V) and Se(II) systems showed fluxional behavior in solution due to the presence of two major rotamers, as evidenced with solution NMR spectroscopy. Using Variable-Temperature NMR (VT NMR) and supported by DFT (Density Functional Theory) calculations and solid-state NMR, the major rotamers in the solid and in solution were identified. All compounds showed a loss of the through-space J_PSe coupling observed in the unoxidized P(III) and Se(II) systems due to the sequestration of the lone pair of the phosphine, which has been previously identified as the major contributor to the coupling pathway. Full article

In this review, the complete tautomeric equilibria are derived for disubstituted pyrimidine nucleic acid bases starting from phenol, aniline, and their model compounds—monosubstituted aromatic azines. The differences in tautomeric preferences for isolated (gaseous) neutral pyrimidine bases and their model compounds are discussed in light of different functional groups, their positions within the six-membered ring, electronic effects, and intramolecular interactions. For the discussion of tautomeric preferences and for the analysis of internal effects, recent quantum-chemical results are taken into account and compared to some experimental ones. For each possible tautomer-rotamer of the title compounds, the bond length alternation, measured by means of the harmonic oscillator model of electron delocalization (HOMED) index, is examined. Significant HOMED similarities exist for mono- and disubstituted derivatives. The lack of parallelism between the geometric (HOMED) and energetic (ΔG) parameters for all possible isomers clearly shows that aromaticity is not the main factor that dictates tautomeric preferences for pyrimidine bases, particularly for uracil and thymine. The effects of one-electron loss (positive ionization) and one-electron gain (negative ionization) on prototropy and bond length alternation are also reviewed for pyrimidine bases and their models. Full article

Amino acid substitutions and post-translational modifications (PTMs) play a crucial role in many cellular processes by directly affecting the structural and dynamic features of protein interaction. Despite their importance, the understanding of protein PTMs at the structural level is still largely incomplete. The Protein Data Bank contains a relatively small number of 3D structures having post-translational modifications. Although recent years have witnessed significant progress in three-dimensional modeling (3D) of proteins using neural networks, the problem related to predicting accurate PTMs in proteins has been largely ignored. Predicting accurate 3D PTM models in proteins is closely related to another fundamental problem: predicting the correct side-chain conformations of amino acid residues in proteins. An analysis of publications as well as the paid and free software packages for modeling three-dimensional structures showed that most of them focus on working with unmodified proteins and canonical amino acid residues; the number of articles and software packages placing emphasis on modeling three-dimensional PTM structures is an order of magnitude smaller. This paper focuses on modeling the side-chain conformations of proteins containing PTMs (nonstandard amino acid residues). We collected our own libraries comprising the most frequently observed PTMs from the PDB and implemented a number of algorithms for predicting the side-chain conformation at modification points and in the immediate environment of the protein. A comprehensive analysis of both the algorithms per se and compared to the common Rosetta and FoldX structure modeling packages was also carried out. The proposed algorithmic solutions are comparable in their characteristics to the well-known Rosetta and FoldX packages for the modeling of three-dimensional structures and have great potential for further development and optimization. The source code of algorithmic solutions has been deposited to and is available at the GitHub source. Full article

The conformational landscapes of two highly flexible monosaccharide derivatives, namely phenyl β-D-glucopyranoside (ph-β-glu) and 4-(hydroxymethyl)phenyl β-D-glucopyranoside, also commonly known as gastrodin, were explored using a combined experimental and theoretical approach. For the infrared, Raman, and the associated vibrational optical activity (VOA), i.e., vibrational circular dichroism and Raman optical activity, experiments of these two compounds in DMSO and in water were carried out. Extensive and systematic conformational searches were performed using a recently developed conformational searching tool called CREST (conformer-rotamer ensemble sampling tool) in the two solvents. Fourteen and twenty-four low-energy conformers were identified at the DFT level for ph-β-glu and gastrodin, respectively. The spectral simulations of individual conformers were done at the B3LYP-D3BJ/def2-TZVPD level with the polarizable continuum model of the solvents. The VOA spectral features exhibit much higher specificity to conformational differences than their parent infrared and Raman. The excellent agreements achieved between the experimental and simulated VOA spectra allow for the extraction of experimental conformational distributions of these two carbohydrates in solution directly. The experimental percentage abundances based on the hydroxymethyl (at the pyranose ring) conformations G+, G-, and T for ph-β-glu were obtained to be 15%, 75%, and 10% in DMSO and 53%, 40%, and 7% in water, respectively, in comparison to the previously reported gas phase values of 68%, 25%, and 7%, highlighting the important role of solvents in conformational preferences. The corresponding experimental distributions for gastrodin are 56%, 22%, and 22% in DMSO and 70%, 21%, and 9% in water. Full article