Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions.

Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.

Protection-Free, Two-step Synthesis of C5-C Functionalized Pyrimidine Nucleosides.

A simple, reliable, and efficient method for the gram-scale chemical synthesis of pyrimidine nucleosides functionalized with C5-carboxyl, nitrile, ester, amide, or amidine, starting from unprotected uridine and cytidine, is described. The protocol involves the synthesis of 5-trifluoromethyluridine and 5-trifluoromethylcytidine with Langlois reagent (CF3 SO2 Na) in the presence of tert-butyl hydroperoxide and subsequent transformation of the CF3 group to the C5-C 'carbon substituents' under alkaline conditions. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Synthesis and characterization of 5-trifluoromethyluridine (5-CF3 U) and 5-trifluoromethylcytidine (5-CF3 C) Basic Protocol 2: Conversion of 5-CF3 U and 5-CF3 C to several C5-substituted ribonucleosides.

Ionic Liquid-Supported Photocatalysts: A Reusable Environmentally Friendly Oxidation Reaction System That Uses Air and Light.

Ionic liquids are used in various fields due to their unique physical properties and are widely utilized as reaction solvents in the field of synthetic organic chemistry. We have previously proposed a new organic synthetic method in which the catalyst and reaction reagents are supported on ionic liquids. This method has various advantages, such as the ability to reuse the reaction solvent and catalyst and its facile post-reaction treatment. In this paper, we describe the synthesis of an ionic liquid-supported anthraquinone photocatalyst and the synthesis of benzoic acid derivatives using this system. This synthesis of benzoic acid derivatives via the cleavage of vicinal diols by an ionic liquid-supported anthraquinone photocatalyst is an environmentally friendly process, and furthermore, it has a simple post-reaction process, and the catalyst and solvent can both be reused. To the best of our knowledge, this is the first report on the synthesis of benzoic-acid derivatives via the cleavage of vicinal diols using light and an ionic-liquid-supported catalyst.

[Exhaustive Syntheses of Deuterium-labelled Compounds].

Deuterium (2H, D) is a stable isotope of hydrogen (1H). Deuterium-incorporated (labelled) compounds are widely utilized in various scientific fields such as mechanistic studies of organic reactions, elucidation of drug metabolism, application as tracers for microanalysis. Recently, development of heavy drugs and molecular imaging using techniques such as neutron scattering and Raman spectroscopy are spotlighted. We have developed various deuterium-incorporated compounds using D2O as an inexpensive deuterium source to construct novel functional materials. The use of platinum group metals on carbon as catalysts could result in the multi-deuteration of compounds in the mixed solvents of 2-propanol and D2O, and site-selectively deuterated compounds can be synthesized by organocatalytic methods. In this review, the latter deuteration methods using organocatalysts and their applications are summarized. Terminal alkynes smoothly underwent deuterium incorporation by using triethylamine as an organic base or a solid resin possessing the tertiary amine moiety in the same molecule to give mono-deuterated alkynes. These compounds were partially reduced over our prepared specific palladium catalyst under atmospheric D2 gas to produce tri-deuterated alkenes. Achiral or chiral di-deuterated ß-nitro alcohols were also prepared by the organic-base-catalyzed deuteration of nitromethane, followed by nitroaldol reactions in a one pot manner. The mono-deuteration of aromatic aldehyde could be effectively catalyzed by N-heterocyclic carbene. Furthermore, the α-deuteration of aliphatic aldehydes using a basic resin catalyst and the subsequent Knoevenagel condensation with malononitrile could provide γ-deuterium-incorporated α,ß-unsaturated nitrile derivatives. The deuterated compounds thus obtained can be important synthetic precursors to construct the deuterium-incorporated target functional materials.

[Synthetic Studies on Complex Natural Products Based on Development of a Novel Synthetic Method for Heteroaromatic Skeleton].

Among my recent work on the syntheses of complex natural products based on the development of a novel synthetic method for the heteroaromatic skeleton, this article primarily deals with the total syntheses of (+)-CC-1065, isobatzeline A/B, and batzeline A. These syntheses were accomplished via a novel indole synthesis utilizing a ring expansion reaction of benzocyclobutenone oxime sulfonate as the key step. The 1,2-dihydro-3H-pyrrolo[3,2-e]indole segments of (+)-CC-1065 were rapidly constructed via a two-directional double-ring expansion strategy. Highly substituted pyrrolidine-fused common 5-chloro-2-methylthioindoles of isobatzeline A/B and batzeline A were constructed using a ring expansion reaction of benzocyclobutenone oxime sulfonate with NaSMe and a benzyne-mediated cyclization/functionalization reaction.

Application of the All-Hydrocarbon Stapling Technique in the Design of Membrane-Active Peptides.

The threats of drug resistance and new emerging pathogens have led to an urgent need to develop alternative treatment therapies. Recently, considerable research efforts have focused on membrane-active peptides (MAPs), a category of peptides in drug discovery with antimicrobial, anticancer, and cell penetration activities that have demonstrated their potential to be multifunctional agents. Nonetheless, natural MAPs have encountered various disadvantages, which mainly include poor bioavailability, the lack of a secondary structure in short peptides, and high production costs for long peptide sequences. Hence, an "all-hydrocarbon stapling system" has been applied to these peptides and proven to effectively stabilize the helical conformations, improving proteolytic resistance and increasing both the potency and the cell permeability. In this review, we summarized and categorized the advances made using this powerful technique in the development of stapled MAPs. Furthermore, outstanding issues and suggestions for future design within each subcategory were thoroughly discussed.

[Development of Novel Biologically Active Compounds Based on Synthetic Organic Chemistry].

The aging population has had an impact on society in recent decades. Aging-associated health issues are a particularly challenging aspect to regulate. Therefore, the extension of healthy life expectancy by the application of biologically active compounds is an attractive research topic in the fields of medicinal chemistry, chemical biology, and also organic synthesis. Herein, the first total synthesis of acaulide, acaulone A and 10-keto-acaudiol A is described. These compounds were originally isolated from a culture of Acaulium sp. H-JQSF. Acaulide exhibits anti-osteoporosis activity in a prednisolone-induced osteoporotic zebrafish model; hence, this natural product is expected to be a new lead compound for anti-osteoporosis drugs. The characteristic acaulide skeletons were synthesized via late-stage Michael addition inspired by the proposed biosynthetic pathways. The conformational analysis of the 14-membered macrodiolide revealed the specific conformation that enabled the late-stage stereoselective functionalization.

Application of E/Z-Isomerization Technology for Enhancing Processing Efficiency, Health-Promoting Effects, and Usability of Carotenoids: A Review and Future Perspectives.

Carotenoids are naturally occurring pigments whose presence in the diet is beneficial to human health. Moreover, they have a wide range of applications in the food, cosmetic, and animal feed industries. As carotenoids contain multiple conjugated double bonds in the molecule, a large number of geometric (E/Z, trans/cis) isomers are theoretically possible. In general, (all-E)-carotenoids are the most predominant geometric isomer in nature, and they have high crystallinity and low solubility in various mediums, resulting in their low processing efficiency and bioavailability. Technological developments for improving the processing efficiency and bioavailability of carotenoids utilizing the Z-isomerization have recently been gaining traction. Namely, Z-isomerization of carotenoids induces a significant change in their physicochemical properties (e.g., solubility and crystallinity), leading to improved processing efficiency and bioavailability as well as several biological activities. For the practical use of isomerization technology for carotenoids, the development of efficient isomerization methods and an acute understanding of the changes in biological activity are required. This review highlights the recent advancements in various conventional and unconventional methods for carotenoid isomerization, such as thermal treatment, light irradiation, microwave irradiation, and catalytic treatment, as well as environment-friendly isomerization methods. Current progress in the improvement of processing efficiency and biological activity utilizing isomerization technology and an application development of carotenoid Z-isomers for the feed industry are also described. In addition, future research challenges in the context of carotenoid isomerization have been elaborated upon.

[Development of Green Asymmetric Organocatalytic Synthesis].

Organocatalysts, which are less toxic than metal catalysis, as well as inexpensive, environmentally benign, and stable against moisture and oxygen compared to metal-based catalysts, have received considerable attention for being efficient and clean catalysts. With respect to green chemistry, the development of organocatalysis is a significant research subject for a sustainable society. This article reviews studies on the development of novel organocatalysts and the reactions achieved from using them. Focusing on the push-pull ethylene moiety, in which two electron-withdrawing groups (EWGs) were introduced, we proposed that the vinylogous amide proton (N-H) will lead to the design of organocatalysts. We have developed the diaminomethylenemalononitrile (DMM) organocatalysts, which are push-pull ethylenes having two cyano groups as EWGs, and proved that they are effective for highly stereoselective hydrophosphonylation with aldehydes. The catalytic ability of the DMM organocatalyst was demonstrated in the development of the first asymmetric hydrophosphonylation of ketones using organocatalysts. The DMM organocatalyst can be applied to the selective 1,4-addition asymmetric hydrophosphonylation of enones. In addition, we designed and synthesized novel organocatalysts bearing squaramide-sulfonamide motif as multiple hydrogen bond donors. Squaramide-sulfonamide organocatalysts efficiently catalyzed the asymmetric direct vinylogous aldol reactions of furan-2(5H)-one with aldehydes. Successively, we achieved the synthesis of γ,γ-disubstituted-δ-hydroxy-γ-butenolide via asymmetric direct vinylogous aldol reaction of furanone derivatives using the squaramide-sulfonamide organocatalysts.

Smart chemistry of enzyme immobilization using various support matrices - A review.

The surface chemistry, pendent functional entities, and ease in tunability of various materials play a central role in properly coordinating with enzymes for immobilization purposes. Due to the interplay between the new wave of support matrices and enzymes, the development of robust biocatalytic constructs via protein engineering expands the practical scope and tunable catalysis functions. The concept of stabilization via functional entities manipulation, the surface that comprises functional groups, such as thiol, aldehyde, carboxylic, amine, and epoxy have been the important driving force for immobilizing purposes. Enzyme immobilization using multi-functional supports has become a powerful norm and presents noteworthy characteristics, such as selectivity, specificity, stability, resistivity, induce activity, reaction efficacy, multi-usability, high catalytic turnover, optimal yield, ease in recovery, and cost-effectiveness. There is a plethora of literature on traditional immobilization approaches, e.g., intramolecular chemical (covalent) attachment, adsorption, encapsulation, entrapment, and cross-linking. However, the existing literature is lacking state-of-the-art smart chemistry of immobilization. This review is a focused attempt to cover the literature gap of surface functional entities that interplay between support materials at large and enzyme of interest, in particular, to tailor robust biocatalysts to fulfill the growing and contemporary needs of several industrial sectors.

[Studies on the Syntheses of Bioactive Natural Products Having a Fused Ring System Based on Novel Skeletal Construction Methods].

Here, I describe a part of our efforts to develop synthetic strategies to construct bioactive natural products having a fused ring system. We have designed four chiral building blocks bearing contiguous quaternary stereocenters for the syntheses of bioactive C17-oxygenated steroids/triterpenoids and C9-oxygenated labdane diterpenoids. The compounds were stereoselectively synthesized from α-substituted glycolic acid (R)-3-methylcyclohex-2-enyl esters through Ireland-Claisen rearrangement to construct the stereocenters simultaneously. Synthetic utility of a ß-type building block is highlighted by total syntheses of marrubiin (11 steps, 22%) and related seven labdane diterpene lactones, cyllenine C (12 steps, 29%), marrulactone (13 steps, 11%), marrulanic acid (14 steps, 10%), marrubasch F (12 steps, 14%), marrulibacetal (14 steps, 4%), marrulibacetal A (14 steps, 2%), and desertine (15 steps, 0.5%). These syntheses feature the construction of the [6.6.5]-tricyclic ring portion via a Pauson-Khand reaction, cleavage of the resultant cyclopentenone ring and an elongation of the C9 side chain by an epoxide opening reaction. The relative stereochemistry of desertine was determined to be 13R, 14S, 15S, 16R by some chemical conversions and NMR analysis. Further efforts toward total syntheses of oxygenated terpenoids using three other chiral building blocks and structure-activity relationship study of synthesized labdane diterpene lactones are currently underway in our laboratory and will be reported in due course.

Synthesis of Isothiocyanates Using DMT/NMM/TsO- as a New Desulfurization Reagent.

Thirty-three alkyl and aryl isothiocyanates, as well as isothiocyanate derivatives from esters of coded amino acids and from esters of unnatural amino acids (6-aminocaproic, 4-(aminomethyl)benzoic, and tranexamic acids), were synthesized with satisfactory or very good yields (25-97%). Synthesis was performed in a "one-pot", two-step procedure, in the presence of organic base (Et3N, DBU or NMM), and carbon disulfide via dithiocarbamates, with 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium toluene-4-sulfonate (DMT/NMM/TsO-) as a desulfurization reagent. For the synthesis of aliphatic and aromatic isothiocyanates, reactions were carried out in a microwave reactor, and selected alkyl isothiocyanates were also synthesized in aqueous medium with high yields (72-96%). Isothiocyanate derivatives of L- and D-amino acid methyl esters were synthesized, under conditions without microwave radiation assistance, with low racemization (er 99 > 1), and their absolute configuration was confirmed by circular dichroism. Isothiocyanate derivatives of natural and unnatural amino acids were evaluated for antibacterial activity on E. coli and S. aureus bacterial strains, where the most active was ITC 9e.

Solid-Phase Synthesis of an Insect Pyrokinin Analog Incorporating an Imidazoline Ring as Isosteric Replacement of a trans Peptide Bond.

A facile solid-phase synthetic method for incorporating the imidazoline ring motif, a surrogate for a trans peptide bond, into bioactive peptides is reported. The example described is the synthesis of an imidazoline peptidomimetic analog of an insect pyrokinin neuropeptide via a cyclization reaction of an iminium salt generated from the preceding amino acid and 2,4-diaminopropanoic acid (Dap).

Two-stage Enzymatic Hydrolysis of Soybean Concentrated Phospholipid to Prepare Glycerylphosphorylcholine: Optimized by Response Surface Methodology.

A two-stage enzymatic hydrolysis method, in which phospholipase A1 (PLA1) was added after phospholipase A2 (PLA2) was added for a certain time, was successfully carried out to prepare glycerylphosphorylcholine (GPC) from soybean concentrated phospholipid. Effects of reaction variables on hydrolysis reaction were optimized using response surface methodology, and the optimal conditions were as follows: PLA2 load of 1.25%, PLA1 load of 0.70%, substrate concentration of 13%, reaction temperature of 41°C, and stirring rate of 680 rpm. Under the optimal conditions, the GPC yield reached 83.07%, which is close to the predicted value by the fitted model. This paper not only provides an efficient and low-cost method to prepare GPC, but also improves the high-value utilization of soybean concentrated phospholipid.

Solidified floating organic drop microextraction (SFODME) for the simultaneous analysis of three non-steroidal anti-inflammatory drugs in aqueous samples by HPLC.

In this work, a liquid-liquid microextraction methodology using solidified floating organic drop (SFODME) was combined with liquid chromatography and UV/Vis detection to determine non-steroidal anti-inflammatory drugs (NSAIDs) naproxen (NPX), diclofenac (DCF), and mefenamic acid (MFN) in tap water, surface water, and seawater samples. Parameters that can influence the efficiency of the process were evaluated, such as the type and volume of the extractor and dispersive solvents, effect of pH, agitation type, and ionic strength. The optimized method showed low detection limits (0.09 to 0.25 µg L-1), satisfactory recovery rates (90 to 116%), and enrichment factors in the range between 149 and 199. SFODME showed simplicity, low cost, speed, and high concentration capacity of the analytes under study. Its use in real samples did not demonstrate a matrix effect that would compromise the effectiveness of the method, being possible to apply it successfully in water samples with different characteristics.

Preface from the Guest Editor of Special Issue "Simple Substances of Non-Metals: Molecular Structures Modeling with Using DFT and More Advanced Methods of Quantum Chemistry".

According to the traditional definition of the concept of "simple substance" adopted in chemistry, it is as a chemical compound, the structural unit of which (molecule, ion, radical, the link of the polymer chain, the unit cell of the crystal lattice, etc [...].

En Route to the Transformation of Glycoscience: A Chemist's Perspective on Internal and External Crossroads in Glycochemistry.

Carbohydrate chemistry is an essential component of the glycosciences and is fundamental to their progress. This Perspective takes the position that carbohydrate chemistry, or glycochemistry, has reached three crossroads on the path to the transformation of the glycosciences, and illustrates them with examples from the author's and other laboratories. The first of these potential inflexion points concerns the mechanism of the glycosylation reaction and the role of protecting groups. It is argued that the experimental evidence supports bimolecular SN2-like mechanisms for typical glycosylation reactions over unimolecular ones involving stereoselective attack on naked glycosyl oxocarbenium ions. Similarly, it is argued that the experimental evidence does not support long-range stereodirecting participation of remote esters through bridged bicyclic dioxacarbenium ions in organic solution in the presence of typical counterions. Rational design and improvement of glycosylation reactions must take into account the roles of the counterion and of concentration. A second crossroads is that between mainstream organic chemistry and glycan synthesis. The case is made that the only real difference between glycan and organic synthesis is the formation of C-O rather than C-C bonds, with diastereocontrol, strategy, tactics, and elegance being of critical importance in both areas: mainstream organic chemists should feel comfortable taking this fork in the road, just as carbohydrate chemists should traveling in the opposite direction. A third crossroads is that between carbohydrate chemistry and medicinal chemistry, where there are equally many opportunities for traffic in either direction. The glycosciences have advanced enormously in the past decade or so, but creativity, input, and ingenuity of scientists from all fields is needed to address the many sophisticated challenges that remain, not the least of which is the development of a broader and more general array of stereospecific glycosylation reactions.

Recent Advances in Rapid Synthesis of Non-proteinogenic Amino Acids from Proteinogenic Amino Acids Derivatives via Direct Photo-Mediated C-H Functionalization.

Non-proteinogenic amino acids have attracted tremendous interest for their essential applications in the realm of biology and chemistry. Recently, rising C-H functionalization has been considered an alternative powerful method for the direct synthesis of non-proteinogenic amino acids. Meanwhile, photochemistry has become popular for its predominant advantages of mild conditions and conservation of energy. Therefore, C-H functionalization and photochemistry have been merged to synthesize diverse non-proteinogenic amino acids in a mild and environmentally friendly way. In this review, the recent developments in the photo-mediated C-H functionalization of proteinogenic amino acids derivatives for the rapid synthesis of versatile non-proteinogenic amino acids are presented. Moreover, postulated mechanisms are also described wherever needed.

Optimization and Characterization of Mesoporous Sulfonated Carbon Catalyst and Its Application in Modeling and Optimization of Acetin Production.

In this study, an optimized mesoporous sulfonated carbon (OMSC) catalyst derived from palm kernel shell biomass was developed using template carbonization and subsequent sulfonation under different temperatures and time conditions. The OMSC catalyst was characterized using acid-base titration, elemental analysis, XRD, Raman, FTIR, XPS, TPD-NH3, TGA-DTA, SEM, and N2 adsorption-desorption analysis to reveal its properties. Results proved that the OMSC catalyst is mesoporous and amorphous in structure with improved textural, acidic, and thermal properties. Both FTIR and XPS confirmed the presence of -SO3H, -OH, and -COOH functional groups on the surface of the catalyst. The OMSC catalyst was found to be efficient in catalyzing glycerol conversion to acetin via an acetylation reaction with acetic acid within a short period of 3 h. Response surface methodology (RSM), based on a two-level, three-factor, face-centered central composite design, was used to optimize the reaction conditions. The results showed that the optimized temperature, glycerol-to-acetic acid mole ratio, and catalyst load were 126 °C, 1:10.4, and 0.45 g, respectively. Under these optimum conditions, 97% glycerol conversion (GC) and selectivities of 4.9, 27.8, and 66.5% monoacetin (MA), diacetin (DA), and triacetin (TA), respectively, were achieved and found to be close to the predicted values. Statistical analysis showed that the regression model, as well as the model terms, were significant with the predicted R2 in reasonable agreement with the adjusted R2 (<0.2). The OMSC catalyst maintained excellent performance in GC for the five reaction cycles. The selectivity to TA, the most valuable product, was not stable until the fourth cycle, attributable to the leaching of the acid sites.

NMR Study of Intercalates and Grafted Organic Derivatives of H2La2Ti3O10.

The protonated perovskite-like titanate H2La2Ti3O10 has been used to produce organic-inorganic hybrids with simple organic molecules: methylamine, methanol, monoethanolamine, and n-butylamine. The optimal pathways for the preparation of such hybrids are summarized. Solid-state NMR, combined with thermal analysis, Raman, and IR spectroscopy, has been applied to determine the bonding type in the obtained organic-inorganic hybrids. It has been found that, in the methanolic hybrid, the organic residues are covalently bound to the inorganic matrix. In contrast, in the methylamine and n-butylamine hybrids, the organic molecules are intercalated into the inorganic matrix in cationic forms. The structure of the monoethanolamine hybrid is composite and includes both the covalently bound and intercalated organic species.