A structural study of fentanyl by DFT calculations, NMR and IR spectroscopy

Design, spectroscopic analysis, DFT calculations, adsorption evaluation, molecular docking, comprehensive in silico and in vitro bioactivity studies of thiocarbohydrazide grafted dialdehyde cellulose nanobiosorbent

Heavy metals have attracted considerable attention lately because of their widespread occurrence in aquatic environments and potential biological toxicity to animals and human. The current investigation focused on synthesizing the DAC@TCH nanobiosorbent by coupling dialdehyde cellulose with thiocarbohydrazide ligand. Subsequent characterization of DAC@TCH was carried out utilizing various analytical methods such as elemental analysis, scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared (FT-IR), and thermogravimetric analysis (TGA and DTA). DFT calculations were utilized to verify the molecular structure, analysis of frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) and reactivity descriptor for all phases. In vitro experiments were conducted to evaluate the biological properties of the DAC@TCH nanobiosorbent. These findings revealed that the synthesized DAC@TCH nanobiosorbent has been observed to show effective antibacterial IZD value against E. Coli (28 mm) which is superior to the efficacy of standard drug amoxicillin used (5 mm). Furthermore, in silico antibacterial activities (molecular docking) of the DAC@TCH have indicated this to exhibit excellent efficacy with docking score of (-7.4237 kcal/mol) and (-7.1325 kcal/mol) for S. aureus and, E. coli, respectively. Meanwhile the binding energies (best docking scores) in kcal/mol for Amoxicillin are (-5.8090) and (-6.7442) for S. aureus and, E. coli, respectively. Drug-likeness rules like Lipinski's, Veber's and Egan's were considered for a more comprehensive evaluation. The prepared DAC@TCH nanobiosorbent was investigated for its potential to adsorb metal ions (Ag+, Hg2+, and Cu2+) from diverse water samples. Optimal conditions including pH, temperature, DAC@TCH dosage, oscillation time, initial metal ion concentration, and interference from other ions were explored. The adsorption of Hg2+, Cu2+, and Ag+ ions by DAC@TCH followed pseudo-second-order kinetics and Langmuir isothermal model, achieving maximum adsorption capacities of 196 mg/g for Ag+, 190 mg/g for Hg2+, and 73 mg/g for Cu2+. The adsorption process was determined to be exothermic and spontaneous across varying temperatures. Additionally, over 95% of adsorbed metal ions were effectively desorbed using thiourea (5%) and 0.3 M HNO3 elution mixture. DAC@TCH nanobiosorbent demonstrated excellent reusability, retaining its adsorption capacity through five cycles without degradation. The study highlights the potential of DAC@TCH for efficient recovery of heavy metals from different water sources, considering its application versatility, reusability, and minimal interference. Furthermore, the plausible mechanism of Ag+, Hg2+, and Cu2+ adsorption onto DAC@TCH bionanosorbent is elucidated.

Synthesis, Antibacterial, and Antibiofilm Activities of Imidazo[2,1-b]Thiazole Chalcone Derivatives: In Vitro and In Silico Studies

In recent years, imidazothiazole-chalcone conjugates have emerged as notable pharmacophores with potential applications in discovering biologically active compounds. This study focuses on synthesizing novel imidazo[2,1-b]thiazole chalcone derivatives through a facile and conventional process adhering to several principles of green chemistry, facilitating scalable production. The synthesized compounds underwent comprehensive spectroscopic analysis, including 1H NMR, 13C NMR, LC-MS, and FT-infrared (IR) techniques. Theoretical FT-IR and NMR analysis, frontier molecular orbitals (FMOs), and global reactivity descriptors were calculated and interpreted. Furthermore, molecular electrostatic potential (MEP) surface, Mulliken atomic charge, electron localization function (ELF), localized orbital locator (LOL), and quantum theory of atoms in molecules (QTAIM) were analyzed. The newly synthesized compounds were screened in vitro for their antibacterial and antibiofilm activities. In addition, computational docking studies were performed to gain further insights into molecular interactions and found to support the results.

Advancing the Prediction of MS/MS Spectra Using Machine Learning

Tandem mass spectrometry (MS/MS) is an important tool for the identification of small molecules and metabolites where resultant spectra are most commonly identified by matching them with spectra in MS/MS reference libraries. While popular, this strategy is limited by the contents of existing reference libraries. In response to this limitation, various methods are being developed for the in silico generation of spectra to augment existing libraries. Recently, machine learning and deep learning techniques have been applied to predict spectra with greater speed and accuracy. Here, we investigate the challenges these algorithms face in achieving fast and accurate predictions on a wide range of small molecules. The challenges are often amplified by the use of generic machine learning benchmarking tactics, which lead to misleading accuracy scores. Curating data sets, only predicting spectra for sufficiently high collision energies, and working more closely with experimental mass spectrometrists are recommended strategies to improve overall prediction accuracy in this nuanced field.

Combining surface-enhanced Raman spectroscopy (SERS) and paper spray mass spectrometry (PS-MS) for illicit drug detection

There is an ongoing effort in the US illicit drug market to make new psychoactive compounds more potent and addictive. Due to continuous chemical modifications, many fentanyl analogs are developed and mixed with more traditional illicit drugs, such as cocaine and heroin. Detecting fentanyl and fentanyl analogs in these illicit drug mixtures has become more crucial because of the increased potency and associated health risks. Most confirmatory procedures require time-consuming and expensive, highly sophisticated laboratory equipment and experimental procedures, which can delay critical information that might save a victim or find a suspect. In this study, we propose miniaturizing and accelerating this process by combining surface-enhanced Raman spectroscopy (SERS) analysis and paper spray mass spectrometry (PS-MS). For this aim, dual-purposed paper substrates were developed through soaking in Au/Ag nanostars suspensions. These novel, in-house prepared paper SERS substrates showed stability for up to four weeks with and without the presence of drug compounds. Fentanyl analogs with similar SERS spectra were differentiated by coupling with PS-MS. The limit of detection (LOD) for fentanyl on the paper substrates is 34 μg/mL and 0.32 μg/mL for SERS and PS-MS, respectively. Fentanyl and fentanyl analogs show selective SERS enhancement that helped to detect trace amounts of these opioids in heroin and cocaine street samples. In short, we propose the combination of SERS/PS-MS by using modified paper substrates to develop cost-effective, sensitive, rapid, portable, reliable, and reproducible methods to detect illicit drugs, especially trace amounts of fentanyl and fentanyl analogs in illicit drug mixtures. The combination of these two category A techniques allows for the identification of illicit drugs according to the SWGDRUG guidelines.

Synthesis, Characterizations, and Quantum Chemical Investigations on Imidazo[1,2-a]pyrimidine-Schiff Base Derivative: (E)-2-Phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine

In this study, (E)-2-phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine (3) is synthesized, and detailed spectral characterizations using 1H NMR, 13C NMR, mass, and Fourier transform infrared (FT-IR) spectroscopy were performed. The optimized geometry was computed using the density functional theory method at the B3LYP/6-311++G(d,p) basis set. The theoretical FT-IR and NMR (1H and 13C) analysis are agreed to validate the structural assignment made for (3). Frontier molecular orbitals, molecular electrostatic potential, Mulliken atomic charge, electron localization function, localized orbital locator, natural bond orbital, nonlinear optical, Fukui functions, and quantum theory of atoms in molecules analyses are undertaken and meticulously interpreted, providing profound insights into the molecular nature and behaviors. In addition, ADMET and drug-likeness studies were carried out and investigated. Furthermore, molecular docking and molecular dynamics simulations have been studied, indicating that this is an ideal molecule to develop as a potential vascular endothelial growth factor receptor-2 inhibitor.

Quantitative Raman Cross-Sections and Band Assignments for Fentanyl and Fentanyl Analogs

Raman cross sections and spectra were measured for five synthetic opioid fentanyl analogs: fentanyl citrate, sufentanil citrate, alfentanil HCl, carfentanil oxalate, and remifentanil HCl. The measurements were performed with excitation wavelengths in the visible (532 nm) and near infrared (785 nm). In addition, density functional theory (DFT) calculations were employed to generate simulated spectra of the compounds and aid in identification of the observed spectral modes. These cross-section measurements and calculations were also used to assess results from a series of measurements of fentanyls cut with other powdered materials. These measurements are valuable for assessment of field-deployable Raman chemical sensors for detection of fentanyl and fentanyl analogs, including when mixed with other materials.

Analysis of indole and indazole amides synthetic cannabinoids by differential Raman spectroscopy based on ANN

A simple, rapid, accurate, and non-destructive method was developed for the determination of cannabinoids, combining principal component analysis and multi-layer perceptron neural network to classify indole and indazole amide synthetic cannabinoids. Under the experimental conditions of this study, 25 experimental samples were successfully classified into two categories as the final classification, which guaranteed 96% correct rate. First, the samples were manually classified and divided into two categories according to the difference in peak position and peak intensity of the differential Raman characteristic peaks at 650-540 cm^-1 , etc. Fisher's discriminant method (FDA) and principal component analysis (PCA) were used to analyze the experimental data. Fisher's discriminant analysis was used to formulate two classification functions to discriminate the results of manual classification, and the overall accuracy rate of classification reached 88%. Principal component analysis was used to reduce the dimensionality of the data, which could reduce the influence of redundant data on the experimental results. The original data, FDA-processed data and PCA-processed data, and artificial neural network algorithm (ANN-MLP/RBF) were combined to build a classification model. In the MLP model, the classification accuracy of the original data, FDA-processed data, and PCA-processed data was 80%, 92%, and 96% respectively, and the overall accuracy of the sample classification was 89.33%. In the RBF model, the accuracy of sample classification was 76%, 84%, and 92% respectively, and the overall accuracy of sample classification was 84%. Differential Raman spectroscopy could be used to distinguish 25 kinds of synthetic cannabinoids, and finally, the samples were divided into two categories. The PCA + MLP model was the best for processing spectral data. Based on the perspective of multivariate data, this study demonstrated that the method could be used for rapid and non-destructive testing of indole and indazole amide synthetic cannabinoids and that an efficient and non-destructive classification model was obtained. This method could be used for rapid detection and inspection of drugs in the field of forensic science.

Computational analyses of the vibrational spectra of fentanyl, carfentanil and remifentanil

The infrared (IR) spectra of fentanyl, carfentanil and remifentanil, and protonated salts, are computed using quantum chemistry methods. New experimental FTIR spectra are also reported and compared to the calculations. The accuracy of two density functional theory methods, B3LYP and M06-2X, are tested against higher level theories (MP2) and the experimental data. Gas phase IR spectra are calculated for both the neutral and protonated molecules in order to compare with the experimental data measured for various salts of fentanyl and its analogues. Key vibrational modes are selected and studied in detail using a vibrational mode locality calculation. The main contributing atomic movements in these vibrational modes are identified.

A possible potential COVID-19 drug candidate: Diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate: Docking of disordered independent molecules of a novel crystal structure, HSA/DFT/XRD and cytotoxicity

This study reports the synthesis, characterization and importance of a novel diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate (MQOAHM). Two independent molecular structures of the disordered MQOAHM have been established by XRD‑single‑crystal analysis in a ratio of 0.596(3)/0.404(3), MQOAHM (a) and MQOAHM (b), respectively. MQOAHM was characterized by means of various spectroscopic tools ESI-MS, IR, ¹H &¹³C NMR analyses. Density Functional Theory (DFT) method, B3LYP, 6-311++G(d,p) basis set was used to optimize MQOAHM molecule. The obtained theoretical structure and experimental structure were superimposed on each other, and the correlation between them was calculated. The Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) were created, and the energy gap between these orbitals was calculated. For analyzing intermolecular interactions, Molecular Electrostatic Potential (MEP) and Hirshfeld Surface Analysis were studied. For a fair comparative study, the two forms of the title compound were docked together with 18 approved drugs and N3 under precisely the same conditions. The disordered molecule structure's binding scores against 7BQY were -7.0 and -6.9 kcal/mol^-1 for MQOAHM (a) and MQOAHM (b), respectively. Both the forms show almost identical superimposed structures and scores indicating that the disorder of the molecule, in this study, has no obvious effect. The high binding score of the molecule was attributed to the multi-hydrogen bond and hydrophobic interactions between the ligand and the receptor's active amino acid residues. Worth pointing out here that the aim of using the free energy in Silico molecular docking approach is to rank the title molecule compared to the wide range of approved drugs and a well-established ligand N3. The binding scores of all the molecules used in this study are ranged from -9.9 to -4.5 kcal/mol^-1. These results and the supporting statistical analyses suggest that this malonate-based ligand merits further research in the context of possible therapeutic agents for COVID-19. Cheap computational techniques, PASS, Way2drug and ADMET, online software tools, were used in this study to uncover the title compound's potential biological activities and cytotoxicity.

Predictive calculation of structural, nonlinear optical, electronic and thermodynamic properties of andirobin molecule from ab initio and DFT methods

The structural, nonlinear optical, electronic and thermodynamic properties of andirobin molecule were carried out by density functional theory at the B3LYP, WB97XD level and at the Restricted Hartree–Fock level by employing 6–311G(d,p) basis set. The obtained values of bond lengths, bond angles, 1H NMR and 13C NMR are in good agreement with experimental values. The dipole moment and first static hyperpolarizability show that andirobin can be applied in nonlinear optical devices. HOMO–LUMO energy gap values were found to be greater than 4 eV and lead us to the conclusion that this molecule can be used as insulator in many electronic devices. The thermal energy (E), molar heat capacity at constant volume $$(C_{v}$$ ( C v ) and entropy (S) were also calculated.

Reductive Amination in the Synthesis of Pharmaceuticals

Reductive amination plays a paramount role in pharmaceutical and medicinal chemistry owing to its synthetic merits and the ubiquitous presence of amines among biologically active compounds. It is one of the key approaches to C-N bond construction due to its operational easiness and a wide toolbox of protocols. Recent studies show that at least a quarter of C-N bond-forming reactions in the pharmaceutical industry are performed via reductive amination. This Review concisely compiles information on 71 medical substances that are synthesized by reductive amination. Compounds are grouped according to the principle of action, which includes drugs affecting the central nervous system, drugs affecting the cardiovascular system, anticancer drugs, antibiotics, antiviral and antifungal medicines, drugs affecting the urinary system, drugs affecting the respiratory system, antidiabetic medications, drugs affecting the gastrointestinal tract, and drugs regulating metabolic processes. A general synthetic scheme is provided for each compound, and the description is focused on reductive amination steps. The green chemistry metric of reaction mass efficiency was calculated for all reactions.

Vibrational spectral analysis, XRD-structure, computation, exo⇔endo isomerization and non-linear optical crystal of 5-((5-chloro-1H-indol-2-yl)methylene)-1,3-diethyl-2-thioxodihy-dropyrimidine-4,6 (1H,5H)-dione

This work deals with the synthesis and characterization of the novel 5-((5-chloro-1H-indol-2-yl)methylene)-1,3-diethyl-2-thioxodihydro-pyrimidine-4,6(1H,5H)-dione π-bridge (D–A–D) donor–acceptor–donor compound. Its exo-isomer structure has been proven by XRD-single-crystal analysis for the first time. The IR, UV–Vis., MS, CHN-, ¹H and ¹³C NMR analysis were also carried out. The DFT-optimized structural-parameters were matched with the XRD-crystallographic data. The experimental-XRD-interactions in the lattice were compared to the computed Hirshfeld analysis (HSA), MEP map and Mulliken charge population. The DFT/6-311G(d) calculations like IR/B3LYP, TD-SCF, HOMO–LUMO, GRD and GIAO-NMR have been compared to their corresponding experimental parameters. Non-linear optical (NLO) crystal theoretical-analysis was carried out then compared to urea reference. The compound thermal activity was evaluated in an open-atmosphere by TG/DTG analysis.

Quantum chemical insight into the molecular structure of L-chemosensor 1,3-dimethyl-5-(thien-2-ylmethylene)-pyrimidine-2,4,6-(1H,3H,5H)-trione: Naked-eye colorimetric detection of copper(II) anions

A sensitive colorimetric L-chemosensor 1,3-dimethyl-5-(thien-2-ylmethylene)-pyrimidine-2,4,6-(1[Formula: see text]-trione was developed by Knoevenagel combination of barbituric acid with thiophene aldehyde chelating moiety. The sensor displayed a high colorimetric Cu(II)X2 response; a dramatic methanol color change was recorded depending on anion type ([Formula: see text], Cl[Formula: see text], ClO[Formula: see text], NO[Formula: see text], OAc[Formula: see text], and SO[Formula: see text]. Off-on-off decolorized halochromism of the L-chemosensor/CuBr2 was recorded in an acidic medium. The structure of the L-chemosensor was confirmed by single-crystal X-ray diffraction, elemental analysis, and molecular spectroscopic tools such as UV–Vis, Fourier transform infra-red, 1H, and [Formula: see text]C nuclear magnetic resonance (NMR) spectroscopy. The thermal stability of the L-chemosensor was experimentally evaluated by thermogravimetric analysis. The structural optimized parameters of the ligand matched the crystallographic data, and the intermolecular forces were computed by Hirshfeld surface analysis. Electronic absorption in several solvents and 1H NMR were correlated with the computed spectra in the gaseous state. The HOMO/LUMO, global reactivity descriptor quantum parameters, Mulliken charge population, and molecular electrostatic potential of the L-chemosensor were also computed.