Green Chemistry in the Synthesis of Pharmaceuticals.

The principles of green chemistry (GC) can be comprehensively implemented in green synthesis of pharmaceuticals by choosing no solvents or green solvents (preferably water), alternative reaction media, and consideration of one-pot synthesis, multicomponent reactions (MCRs), continuous processing, and process intensification approaches for atom economy and final waste reduction. The GC's execution in green synthesis can be performed using a holistic design of the active pharmaceutical ingredient's (API) life cycle, minimizing hazards and pollution, and capitalizing the resource efficiency in the synthesis technique. Thus, the presented review accounts for the comprehensive exploration of GC's principles and metrics, an appropriate implication of those ideas in each step of the reaction schemes, from raw material to an intermediate to the final product's synthesis, and the final execution of the synthesis into scalable industry-based production. For real-life examples, we have discussed the synthesis of a series of established generic pharmaceuticals, starting with the raw materials, and the intermediates of the corresponding pharmaceuticals. Researchers and industries have thoughtfully instigated a green synthesis process to control the atom economy and waste reduction to protect the environment. We have extensively discussed significant reactions relevant for green synthesis, one-pot cascade synthesis, MCRs, continuous processing, and process intensification, which may contribute to the future of green and sustainable synthesis of APIs.

5-Amino-1,2,4-triazol-3-one Degradation by Indirect Photolysis: A Density Functional Theory Study.

Sunlight irradiation induces formation of reactive oxygen species (superoxide, hydroperoxyl radical, singlet oxygen, etc.), which readily take part in degradation of environmental pollutants. Being a primary ingredient in a suite of insensitive munition formulations, NTO (5-nitro-1,2,4-triazol-3-one) can be released onto training range soils and reduced to ATO (5-amino-1,2,4-triazol-3-one) by soil bacteria or iron-contained minerals. ATO can be dissolved in surface water and groundwater due to its good water solubility and then undergo further decomposition. A detailed investigation of possible mechanisms for ATO decomposition in water induced by superoxide, hydroperoxyl radical, and singlet oxygen as pathways for ATO environmental degradation was performed by computational study at the PCM(Pauling)/M06-2X/6-311++G(d,p) level. Hydrolysis and degradation of ATO induced by superoxide are unlikely to occur due to the high activation energy or endergonicity of the processes. The hydroperoxyl radical causes rapid and reversible hydrogen transfer from ATO, while an attachment of the hydroperoxyl radical to ATO can induce decomposition of ATO, leading to its mineralization. Singlet oxygen shows a higher reactivity toward ATO than the hydroperoxyl radical. Decomposition of ATO was found to be a multistep process that begins with singlet oxygen attachment to the carbon atom of the C═N double bond. The intermediate that is formed undergoes recyclization, cycle opening, and sequential elimination of nitrogen gas, ammonia, and carbon(IV) oxide. Isocyanic acid, which arises intermediately, hydrolyzes into ammonia and carbon(IV) oxide. Calculated activation energies and high exergonicity of the studied processes support the contribution of singlet oxygen and the hydroperoxyl radical to ATO degradation into low-weight inorganic compounds in the environment.

Designing Thiadiazoloquinoxaline-Based Conjugated Polymers for Efficient Organic Photovoltaics: A DFT/TDDFT Study.

Clean and renewable energy development is becoming frontier research for future energy resources, as renewable energy offers sustainable and environmentally friendly alternatives to non-renewable sources such as fossil fuels. Among various renewable energy sources, tremendous progress has been made in converting solar energy to electric energy by developing efficient organic photovoltaics. Organic photovoltaic materials comprising conjugated polymers (CP) with narrow optical energy gaps are promising candidates for developing sustainable sources due to their potentially lower manufacturing costs. Organic semiconductor materials with a high electron affinity are required for many optoelectronic applications. We have designed a series of organic semiconductors comprised of cyclopentadithiophene as a donor and thiadiazoloquinoxaline (TQ) as an acceptor, varying the π-conjugation and TQ-derivatives. We have employed density functional theory (DFT) and time-dependent DFT (TDDFT) to evaluate the designed CP's optoelectronic properties, such as optical energy gap, dipole moment, and absorption spectra. Our DFT/TDDFT result shows that the energy gap of CPs is lowered and redshifted in the absorption spectra if there is no insertion of conjugation units such as thiophene and selenophene between donor and acceptor. In addition, selenophene shows relatively better redshift behavior compared to thiophene. Our work also provides rational insight into designing donor/acceptor-based CPs for organic solar cells.

Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism.

To combat mischievous coronavirus disease followed by continuous upgrading of therapeutic strategy against the antibody-resistant variants, the molecular mechanistic understanding of protein-drug interactions is a prerequisite in the context of target-specific rational drug development. Herein, we attempt to decipher the structural basis for the inhibition of SARS-CoV-2 main protease (Mpro) through the elemental analysis of potential energy landscape and the associated thermodynamic and kinetic properties of the enzyme-inhibitor complexes using automated molecular docking calculations in conjunction with classical force field-based molecular dynamics (MD) simulations. The crux of the scalable all-atom MD simulations consummated in explicit solvent media is to capture the structural plasticity of the viral enzyme due to the binding of remdesivir analogues and ascertain the subtle interplay of noncovalent interactions in stabilizing specific conformational states of the receptor that controls the biomolecular processes related to the ligand binding and dissociation kinetics. To unravel the critical role of modulation of the ligand scaffold, we place further emphasis on the estimation of binding free energy as well as the energy decomposition analysis by employing the generalized Born and Poisson-Boltzmann models. The estimated binding affinities are found to vary between -25.5 and -61.2 kcal/mol. Furthermore, the augmentation of inhibitory efficacy of the remdesivir analogue crucially stems from the van der Waals interactions with the active site residues of the protease. The polar solvation energy contributes unfavorably to the binding free energy and annihilates the contribution of electrostatic interactions as derived from the molecular mechanical energies.

Degradation of NTO induced by superoxide and hydroperoxyl radicals: a comprehensive DFT study.

Reactive oxygen species, produced in the aquatic environment under sunlight irradiation, actively take part in degradation of environmental pollutants. NTO (5-nitro-1,2,4-triazol-3-one), being a primary ingredient in a suite of insensitive munitions formulations, may be released into training range soils after incomplete detonations and dissolved in surface water and groundwater due to good water solubility. A detailed investigation of a possible mechanism for NTO decomposition in water induced by superoxide and hydroperoxyl radicals as one of the pathways for NTO environmental degradation was performed with a computational study at the PCM(Pauling)/M06-2X/6-311++G(d,p) level. Superoxide causes rapid deprotonation of NTO. Decomposition of NTO induced by hydroperoxyl radicals was found to be a multistep process leading to mineralization of the nitrocompound. The reaction process may begin with hydroperoxyl radical attachment to carbon atom of the CN double bond of NTO, then proceeds through rupture of C-N bonds and addition of water molecules leading to the formation of nitrous acid, ammonia, nitrogen gas, hydrazine, and carbon(IV) oxide. The obtained results indicate that the anionic form of NTO shows a higher reactivity towards hydroperoxyl radicals than its neutral form. Excitation of NTO by sunlight enables complete mineralization of NTO induced by superoxide. The calculated activation energies and exergonicity of the studied processes support the contribution of hydroperoxyl radicals and superoxide to the degradation of NTO in the environment into low-weight inorganic compounds.

Role of Hydroxyl Radical in Degradation of NTO: DFT Study.

Hydroxyl radicals are important reactive oxygen species produced in the aquatic environment under sunlight irradiation. Many organic pollutants may be decomposed as they encounter hydroxyl radicals, due to their high oxidative ability. NTO (5-nitro-1,2,4-triazol-3-one), an energetic material used in military applications, may be released to the environment and dissolved in surface water and groundwater due to its good water solubility. A detailed investigation of the possible mechanism for NTO decomposition in water induced by hydroxyl radical as one of the pathways for NTO environmental degradation was performed by computational study at the PCM/M06-2X/6-311++G(d,p) level. Decomposition of NTO was found to be a multistep process that may begin with an addition of hydroxyl radical to the carbon atom of C═N double bond and consequent release of a nitrite radical. The formed intermediate undergoes a series of chemical transformations that include the attachments of hydroxyl radical to carbon atoms, the transfer of hydrogen to hydroxyl radical, isomerization, and bond cleavage, leading to low-weight inorganic compounds, such as ammonia, nitrogen gas, nitrous acid, nitric acid, and carbon(IV) oxide. The anionic form of NTO is more reactive toward interaction with the hydroxyl radical as compared with its neutral form. Calculated activation energies and high exergonicity of the studied process support the significant contribution of the hydroxyl radical to NTO mineralization in environment.

Role of Molecular Singlet Oxygen in Photochemical Degradation of NTO: DFT Study.

NTO (5-nitro-1,2,4-triazol-3-one), an energetic material used in military applications, may be released to the environment and dissolved in surface water and groundwater due to its good water solubility. Singlet oxygen is an important reactive oxygen species produced in the aquatic environment under sunlight irradiation. A detailed investigation of the possible mechanism for NTO decomposition in water induced by singlet oxygen as one of the pathways for NTO environmental degradation was performed by a computational study at PCM(Pauling)/M06-2X/6-311++G(d,p) level. Decomposition of NTO was found to be a multistep process that may begin with singlet oxygen attachment to the carbon atom of the C═N double bond. The formed intermediate undergoes cycle opening, and nitrogen gas, nitrous acid, and carbon (IV) oxide elimination. Isocyanic acid, arisen transiently, hydrolyzes into ammonia and carbon (IV) oxide. The obtained results show a significant increase in reactivity of the anionic form of NTO as compared to its neutral form. The calculated activation energies and high exothermicity of the studied processes support the contribution of singlet oxygen to NTO degradation into low-weight inorganic compounds in the environment.

Impact of Internal Carotid Stenosis Treatment on Cerebral Blood Flow Volume: A Comparative Study between Preoperative and Postoperative Values.

BACKGROUND Among patients with ICA stenosis, there are some cases with elevated, undisrupted, and diminished cerebral blood flow (CBF). The aim of this study was to assess the influence of ICA stenosis treatment on postoperative CBF changes in relation to preoperative CBF values. MATERIAL AND METHODS We qualified 58 patients ≥65 years old (28 males, 30 females, mean age 71.02±6.34 years) for surgical intervention due to symptomatic ≥70% ICA stenosis. In all patients, a flow volume in all extracranial arteries (internal carotid [ICA], external carotid [ECA], and vertebral arteries [VA]) was measured preoperatively and 2-3 days following the surgery. The CBF values were compared with the ones established for a healthy population of the same age. RESULTS Preoperatively, there were 3 subgroups of patients, comparing to healthy population: with elevated CBF - "significant compensation," with undisrupted CBF - "mild compensation," and with diminished CBF - "no compensation." Postoperatively, a significant CBF increase was observed in patients with preoperative "no" and "mild compensation" - 277.18±154.26 ml/min (P=0.0000001) and 221.56±98.8 ml/min (P=0.0000001). In a "significant compensation" group, there was no flow increase observed (CBF change of 2.57±58.5 ml/min, P=0.954) - a redistribution of flow was observed. CONCLUSIONS In patients with lower preoperative CBF values, surgical treatment caused a significant increase in global cerebral inflow, which was more prominent in patients with the lowest preoperative CBF. In patients with high preoperative CBF, surgical treatment resulted in a flow redistribution, but did not cause a CBF increase. Volumetric flow assessment in DUS can predict hemodynamic benefit from surgery in terms of CBF increase.

CORAL: Model of Ecological Impact of Heavy Metals on Soils via the Study of Modification of Concentration of Biomolecules in Earthworms (Eisenia fetida).

The traditional application for quantitative structure-property/activity relationships (QSPRs/QSARs) in the fields of thermodynamics, toxicology or drug design is predicting the impact of molecular features using data on the measurable characteristics of substances. However, it is often necessary to evaluate the influence of various exposure conditions and environmental factors, besides the molecular structure. Different enzyme-driven processes lead to the accumulation of metal ions by the worms. Heavy metals are sequestered in these organisms without being released back into the soil. In this study, we propose a novel approach for modeling the absorption of heavy metals, such as mercury and cobalt by worms. The models are based on optimal descriptors calculated for the so-called quasi-SMILES, which incorporate strings of codes reflecting experimental conditions. We modeled the impact on the levels of proteins, hydrocarbons, and lipids in an earthworm's body caused by different combinations of concentrations of heavy metals and exposure time observed over two months of exposure with a measurement interval of 15 days.

Investigating the Effects of Donors and Alkyne Spacer on the Properties of Donor-Acceptor-Donor Xanthene-Based Dyes.

NIR dyes have become popular for many applications, including biosensing and imaging. For this reason, the molecular switch mechanism of the xanthene dyes makes them useful for in vivo detection and imaging of bioanalytes. Our group has been designing NIR xanthene-based dyes by the donor-acceptor-donor approach; however, the equilibrium between their opened and closed forms varies depending on the donors and spacer. We synthesized donor-acceptor-donor NIR xanthene-based dyes with an alkyne spacer via the Sonogashira coupling reaction to investigate the effects of the alkyne spacer and the donors on the maximum absorption wavelength and the molecular switching (ring opening) process of the dyes. We evaluated the strength and nature of the donors and the presence and absence of the alkyne spacer on the properties of the dyes. It was shown that the alkyne spacer extended the conjugation of the dyes, leading to absorption wavelengths of longer values compared with the dyes without the alkyne group. In addition, strong charge transfer donors shifted the absorption wavelength towards the NIR region, while donors with strong π-donation resulted in xanthene dyes with a smaller equilibrium constant. DFT/TDDFT calculations corroborated the experimental data in most of the cases. Dye 2 containing the N,N-dimethylaniline group gave contrary results and is being further investigated.

The System of Self-Consistent Models: The Case of Henry's Law Constants.

Data on Henry's law constants make it possible to systematize geochemical conditions affecting atmosphere status and consequently triggering climate changes. The constants of Henry's law are desired for assessing the processes related to atmospheric contaminations caused by pollutants. The most important are those that are capable of long-term movements over long distances. This ability is closely related to the values of Henry's law constants. Chemical changes in gaseous mixtures affect the fate of atmospheric pollutants and ecology, climate, and human health. Since the number of organic compounds present in the atmosphere is extremely large, it is desirable to develop models suitable for predictions for the large pool of organic molecules that may be present in the atmosphere. Here, we report the development of such a model for Henry's law constants predictions of 29,439 compounds using the CORAL software (2023). The statistical quality of the model is characterized by the value of the coefficient of determination for the training and validation sets of about 0.81 (on average).

Single site Fe on the (110) surface of γ-Al2O3: insights from a DFT study including the periodic boundary approach.

Examination of the stable (110) surface of γ-alumina reveals that there are three different types of sites available to host a single Fe atom. With the carefully calibrated density functional approach (M12-L/SV), three types of Fe single sites on the (110) surface of γ-alumina have been investigated under the periodic boundary conditions. The most stable Fe replacement site on the (110) surface of γ-alumina has been found to be represented by the tri-coordinated FeI position with the quartet spin state. The replacement of Al by Fe atoms at the Al site leads to charge redistributions of the neighboring O atoms. However, sublayer charge distribution is less affected. A significant contribution of p orbitals of the O atoms in the surface phase to the LUMO has been found for the tri-coordinated FeI substitution on the (110) surface. The corresponding oxygen atoms (OA and OA1) have been activated due to the existence of FeI in their neighborhood. The loosened neighboring AlIII-OA bonds match this activation. This activation of O suggests the existence of an important source of the reactive O during the Fe catalytic oxidation of CO processes.

Theoretical DFT Study on the Mechanisms of CO/CO2 Conversion in Chemical Looping Catalyzed by Calcium Ferrite.

The CO/CO2 conversion mechanism on the calcium ferrite (CFO) surface in chemical looping was explored by a computational study using the density functional theory approach. The CFO catalytic reaction pathway of 2CO + O2 → 2CO2 conversion has been elucidated. Our results show that the Fe center in CFO plays the key role as a catalyst in the CO/CO2 conversion. Two energetically stable spin states of CFO, quintet and septet, serve as the effective catalysts. The presence of the triplet O2 molecule caused the conversion of these two spin-state structures into each other along the catalytic reaction pathway. A double release of CO2 was predicted following this reaction mechanism. The rate-determining step is the formation of the 2CO2-CFO complex (P4) in the quintet state (19.0 kcal/mol). The predicted energy barriers for all the steps suggest that the proposed pathway is plausible.

Therapeutics for COVID-19: from computation to practices-where we are, where we are heading to.

After the 1918 Spanish Flu pandemic caused by the H1N1 virus, the recent coronavirus disease 2019 (COVID-19) brought us to the time of serious global health catastrophe. Although no proven therapies are identified yet which can offer a definitive treatment of the COVID-19, a series of antiviral, antibacterial, antiparasitic, immunosuppressant drugs have shown clinical benefits based on repurposing theory. However, these studies are made on small number of patients, and, in majority of the cases, have been carried out as nonrandomized trials. As society is running against the time to combat the COVID-19, we present here a comprehensive review dealing with up-to-date information of therapeutics or drug regimens being utilized by physicians to treat COVID-19 patients along with in-depth discussion of mechanism of action of these drugs and their targets. Ongoing vaccine trials, monoclonal antibodies therapy and convalescent plasma treatment are also discussed. Keeping in mind that computational approaches can offer a significant insight to repurposing based drug discovery, an exhaustive discussion of computational modeling studies is performed which can assist target-specific drug discovery.

How the CORAL software can be used to select compounds for efficient treatment of neurodegenerative diseases?

Recommendations on the efficient application of CORAL software (http://www.insilico.eu/coral) to establish quantitative structure-property/activity relationships (QSPRs/QSARs) are provided. The predictive potential of the approach has been demonstrated for QSAR models developed for inhibitor concentrations (negative decimal logarithm of IC50) of derivatives of N-methyl-d-aspartate (NMDA) receptor, leucine-rich repeat kinase 2 (LRRK2), and tropomyosin receptor kinase A (TrkA). The above three protein targets are related to various neurodegenerative diseases such as Alzheimer's and Parkinson's. Each model was checked using several splits of the data for the training and the validation sets. The index of ideality of correlation (IIC) represents a tool to improve the predictive potential for an arbitrary model. However, the use of the IIC should be carried out according to rules, described in this work.

Evaluating Donor Effects in Isoindigo-Based Small Molecular Fluorophores.

Small molecular organic fluorophores have garnered significant interest because of their indispensable use in fluorescence imaging (FI) and optoelectronic devices. Herein, we designed triphenylamine (TPA)-capped donor-acceptor-donor (D-A-D)-based fluorophores having a variation at the heterocyclic donor (D) units, 3,4-ethylenedioxythiophene (EDOT), furan (FURAN), thiophene (THIO), and 1-methyl-1H-pyrrole (MePyr), with isoindigo as the core electron acceptor (A) unit. Synthesis of these fluorophores (II-X-TPA) resulted in four symmetrical dye molecules: II-EDOT-TPA, II-FURAN-TPA, II-THIO-TPA, and II-MePyr-TPA, where TPA functioned as a terminal unit and a secondary electron donor group. Photophysical, electrochemical, and computational analyses were conducted to investigate the effect of heterocyclic donor units on the II-X-TPA derivatives. Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations provided insightful features of structural and electronic properties of each fluorophore and correlated well with experimental observations. Electron density distribution maps, overlapping frontier molecular orbital diagrams, and highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) electron transfer indicated intramolecular charge transfer (ICT). Theoretical studies confirmed the experimental HOMO energy trend and demonstrated its crucial importance in understanding each heterocycle's donor ability. Stokes shifts of up to ∼178 nm were observed, whereas absorptions and emissions were shifted deeper into the NIR region, resulting from ICT. Results suggest that this isoindigo fluorophore series has potential as a molecular scaffold for the development of efficient FI agents. The studied fluorophores can be further tuned with different donor fragments to enhance the ICT and facilitate in shifting the optical properties further into the NIR region.

Relative Order of Acidity among Hydroxyl Groups of Oxyluciferin and Emission Light Colors in Aqueous Solution.

The magnitude of the acidity of the oxyluciferin in water in the ground and excited state is investigated, and it is found for the first time using computational approach that the enol group of the phenol-enol species is the most acidic in the ground state, but the deprotonation of the phenol of the phenol-keto form is the most favored in the excited state. The relative order of the acidity among the hydroxyl groups in the oxyluciferin is attributed to the sequence of the O-H bond lengths in the enol and phenol group of the phenol-enol form, and the phenol group of the phenol-keto species. The mechanism of determining the dominant emissive species in the excited state is proposed, and the dependence of emission light colors on the photoexcitation energy is elucidated by the high relative concentration of six chemical forms in the ground state and the absorption efficiency.

Semi-correlations combined with the index of ideality of correlation: a tool to build up model of mutagenic potential.

Mutagenicity is the ability of a substance to induce mutations. This hazardous ability of a substance is decisive from point of view of ecotoxicology. The number of substances, which are used for practical needs, grows every year. Consequently, methods for at least preliminary estimation of mutagenic potential of new substances are necessary. Semi-correlations are a special case of traditional correlations. These correlations can be named as "correlations along two parallel lines." This kind of correlation has been tested as a tool to predict selected endpoints, which are represented by only two values: "inactive/active" (0/1). Here this approach is used to build up predictive models for mutagenicity of large dataset (n = 3979). The so-called index of ideality of correlation (IIC) has been tested as a statistical criterion to estimate the semi-correlation. Three random splits of experimental data into the training, invisible-training, calibration, and validation sets were analyzed. Two models were built up for each split: the first model based on optimization without the IIC and the second model based on optimization where IIC is involved in the Monte Carlo optimization. The statistical characteristics of the best model (calculated with taking into account the IIC) n = 969; sensitivity = 0.8050; specificity = 0.9069; accuracy = 0.8648; Matthews's correlation coefficient = 0.7196 (using IIC). Thus, the use of IIC improves the statistical quality of the binary classification models of mutagenic potentials (Ames test) of organic compounds.

Computational and experimental approach to understanding the structural interplay of self-assembled end-terminated alkanethiolates on gold surfaces.

Applications of self-assembled monolayers (SAMs) on surfaces are prevalent in modern technologies and drives the need for a better understanding of the surface domain architecture of SAMs. To explore structural interaction at the interface between gold surfaces and a hydroxyl-terminated alkanethiol, 11-hydroxy-1-undecanethiol, (C11TH) we have employed a combined computational and experimental approach. Density functional theory (DFT) calculations were carried out on the thiol-gold interface using both the Perdew-Burke-Ernzerhof (PBE) and van der Waals (optB86b) density functionals. Our ab initio molecular dynamics (AIMD) simulations revealed that the interface consists of four different distinguished phases, each with different C11TH orientations. Experiments involved deposition of C11TH SAMs onto gold, with the resultant surfaces examined with X-ray photoelectron spectroscopy (XPS) and ellipsometry. Weighted average projected density of states (PDOS) of the different phases were photoionization cross section corrected and these were confirmed by experimental XPS data. Computed molecular parameters including tilt angles and the thickness of SAMs also agreed with the XPS and ellipsometry results. Hydrogen bonding arising from the terminal hydroxyl groups is the primary factor governing the stability of the four phases. Experimental results from XPS and ellipsometry along with DFT simulation results provide insights into the formation of the different orientations of SAM on Au(111) which will guide future efforts in the self-assembled SAMs architecture for other thiols or metal substrates.

Role of Singlet Oxygen in the Degradation of Selected Insensitive Munitions Compounds: A Comprehensive, Quantum Chemical Investigation.

DNAN (2,4-dinitroanisole), NTO (3-nitro-1,2,4-triazol-5-one), and NQ (nitroguanidine) are important energetic materials used in military applications. They may find their way to the environment during manufacturing, transportation, storage, training, and disposal. A detailed investigation of possible mechanisms for reactions of the nitrocompounds with singlet oxygen, one of the potential methods for their degradation, was performed by computational study using the PCM(Pauling)/M06-2X/6-311++G(d,p) approach. Obtained results suggest that reactivity of the investigated munitions compounds toward singlet oxygen follows the order: DNAN > NTO(anion) > NQ ≫ NTO. DNAN is involved in [4 + 2]-addition with oxygen, and further formation of diepoxide or epoxyketone through diradical intermediates have been predicted. The NTO may undergo intramolecular rearrangement with formation of peroxide compound or nitrite radical elimination, and NQ may be transformed into urea.