Proton Sponge Zwitterions with Positively and Negatively Charged Hydrogen Bonds: Extremely Polar Organic Compounds and Interplay of [NHN]+ and [NHN]- Properties.

Six previously unknown zwitterions with positively and negatively charged [NHN] hydrogen bonds were synthesized by acylation of 4,5-bis(dimethylamino)-1-tosylamino-8-aminonaphthalene with subsequent alkaline treatment of the resulting 8-acylamino derivatives. Using NMR and XRD measurements in conjunction with quantum chemical DFT/PBE1PBE/6-311++G(d,p) calculations, it was shown that the negatively charged [NHN]- bond in such compounds commonly differs from the [NHN]+ bond by significantly lower linearity, higher asymmetry, and moderate to strong paramagnetic shift of the chelated NH proton signal. Among other remarkable findings, the most important are (1) unusually high polarity (µ = 21-26 D) of the obtained zwitterions, (2) sharp difference in structures of the solid 1,8-bis(tosylated) zwitterion (BTZ) grown from MeCN or DMF, and (3) registration for one of the stereoisomers of BTZ with the record short [NHN]- hydrogen bridge (N···N = 2.510 Å) almost reaching the theoretical limit (2.50 Å) for the [NHN]+ hydrogen bond.

Structural peculiarities of tandem repeats and their clinical significance.

While it is well established that a mere 2% of human DNA nucleotides are involved in protein coding, the remainder of the DNA plays a vital role in the preservation of normal cellular genetic function. A significant proportion of tandem repeats (TRs) are present in non-coding DNA. TRs - specific sequences of nucleotides that entail numerous repetitions of a given fragment. In this study, we employed our novel algorithm grounded in finite automata theory, which we refer to as Dafna, to investigate for the first time the likelihood of these nucleotide sequences forming non-canonical DNA structures (NS). Such structures include G-quadruplexes, i-motifs, hairpins, and triplexes. The tandem repeats under consideration in our research encompassed sequences containing 1 to 6 nucleotides per repeated fragment. For comparison, we employed a set of randomly generated sequences of the same length (60 nucleotides) as a benchmark. The outcomes of our research exposed a disparity between the potential for NS formation in random sequences and tandem repeats. Our findings affirm that the propensity of DNA and RNA to form NS is closely tied to various genetic disorders, including Huntington's disease, Fragile X syndrome, and Friedreich's ataxia. In the concluding discussion, we present a proposal for a new therapeutic mechanism to address these diseases. This novel approach revolves around the ability of specific nucleic acid fragments to form multiple types of NS.

Oligonucleotides-transformers for molecular biology and nanoengineering.

In the present review, numerous experimental and theoretical data describing the properties of non-canonical DNA structures (NSs) are analyzed. NSs (G-quadruplex, i-motif, hairpin, and triplex) play an important role in epigenetic processes (including the genetic variability of viruses), are prone to energetically low-cost conformational transformations and can very effectively be used in the design of nanoscale devices. Numerous experimental data have been analyzed in connection with the so-called oligonucleotides-transformers (nucleotide sequences that able to fold not only into one, but also into several NSs). These sequences were recently predicted by our calculations using automata and graph theories ("Dafna" algorithm). Possible applications of the oligonucleotides-transformers in nanoengineering and genetic editing of organisms are considered.

Mechanisms of nitric oxide generation in living systems.

In modern chemical and biochemical studies, special attention is paid to molecular systems capable of generating nitric oxide (NO), which is one of the most important signalling molecules in the body and can trigger a whole cascade of reactions. Despite the importance of this molecule, the mechanisms of its formation in living organisms remain a subject of debate. This review combines the most important methods of releasing NO from endogenous and exogenous sources. The history of endogenous NO donors dates back more than 150 years, since the synthesis of nitroglycerin, which remains the standard vasodilator today, even though it is known that it and many other similar compounds lead to the development of a nitrate tolerance. Particular awareness is devoted to the mechanisms of NO formation without the participation of enzymes, since these methods are most important for creating exogenous sources of NO as drugs. The study of NO formation methods is centred on both the creation of new NO donors and understanding the mechanisms of tolerance to them.

Lithium-Promoted Cycloaddition of Indole-2,3-dienolates and Carbon Disulfide as a One-Pot Route to Thiopyrano[4,3-b]indole-3(5H)-thiones.

A new approach for the annulation of a thiopyrane ring to an indole core under mild conditions was developed. Treating 2-methyl-3-acylindoles with lithium diisopropyl amide leads to the elimination of a proton from the 2-methyl group. The lithium indole-2,3-dienolates obtained were found to react with CS2 to give the corresponding thiopyrano[4,3-b]indole-3(5H)-thiones. The mechanism represents a stepwise addition through ion-pair formation, according to PCM/B3LYP/6-311++G**, PBE1PBE/6-311++G**, and MP2//HF/6-311++G** quantum chemical calculations. AIM calculations revealed the essential role of the Li atom at all stages of the process.

From 3-Acyl-2-methylindoles to γ-Carbolines: Li-Promoted Cycloaddition Reaction and Its Quantum Chemical Study.

A one-pot cycloaddition strategy for obtaining γ-carbolines under mild conditions was developed. The reaction represents a new approach to the annulation of a pyridine ring to an indole core. Treating 2-methyl-3-benzoylindoles with lithium diisopropyl amide leads to the elimination of a proton from the 2-methyl group. The organolithium compounds generated were found to react with nitriles. The resulting 4,5-dihydro-1H-pyrido[4,3-b]indol-1-ols undergo spontaneous water elimination to give the corresponding γ-carbolines. The applicability of this reaction for the synthesis of isoquinolines has been shown. For the first time, a lithium atom was found to be part of an eight-centered polycyclic transition state according to a detailed DFT PCM/DFT/B3LYP/6-311++G(d,p) and ab initio PCM/MP2//HF/6-311++G(d,p) quantum chemical study.

Comprehensive study of nitrofuroxanoquinolines. New perspective donors of NO molecules.

The goal of present work is the study of NO releasing mechanisms in nitrofuroxanoquinoline (NFQ) derivatives. Mechanisms of their structural non-rigidity and pathways of NO donation - spontaneous or under the action of sulfanyl radicals or photoirradiation - were considered in details, both experimentally and quantum chemically. Furoxan-containing systems of the discussed type are not capable of spontaneous or photoinduced decomposition under mild conditions, and sulfanyl (radical) induced processes are the most preferable. It was shown that appropriate modification of NFQ through [3 + 2] cycloaddition and subsequent aromatization is a powerful tool to design new prospective donors of NO molecule. Two newly obtained NFQ derivatives were proven to have unusually high NO activity in full accordance with the theoretical model. We hope that these examples will encourage community to seek for new NO active molecules among cycloadducts and modified furoxanes.

Non-canonical DNA structures: Comparative quantum mechanical study.

A study of relative thermodynamic stability of non-canonical DNA structures (triplexes, G-quadruplexes, i-motifs) for the first time was conducted on the basis of quantum chemical DFT/B3LYP/6-31++G (d) calculations. Results of the calculations completely reproduce the experimental data on stability of G-quadruplexes comparatively Watson-Crick B-DNA. It was discovered that combinations of non-canonical DNA structures were energetically more favorable than separated nitrogenous bases. Supramolecular complexes of the non-canonical DNA structures (NSs) can be considered as a biological drug targets in gene regulation (for example in tumor therapy), in contrast to previous works, where NSs were studied independently.

Charge Transfer Complexes Formed by Heterocyclic Thioamides and Tetracyanoethylene: Experimental and Theoretical Study.

Tetracyanoethylene (TCNE) as one of the most versatile organic compounds is involved in various chemical reactions with electron transfer. Charge transfer complexes (CTCs) of a few antioxidants, nitrogen containing thioamides [pyrrolidine-2-thione (I), 1,3-H-imidazolidine-2-thione (II), 1,3-H-Imidazoline-2-thione (III), pyridine-2-thione (IV), 5-trifluoromethylpyridine-2-thione (V), 4-trifluoromethylpyrimidine-2-thione (VI), quinoline-2-thione (VII), 3,4,5,6-tetrahydropyrimidine-2-thione (VIII)] as π-donors and TCNE as π-acceptor were studied. The DFT PCM/UB3LYP/6-31++G(d,p) and SA-CASSCF quantum chemical calculations were used to study the structures and relative stabilities of these complexes in the ground and lowest excited electronic states. The formation of a weak molecular associates in the chloroform and acetonitrile solutions was confirmed by UV/vis and IR absorption spectroscopy. The stability constants and molar extinction coefficients were estimated by UV/vis spectroscopy. The highest stability in acetonitrile is found for associates formed by quinoline-2-thione and pyridine-2-thione with TCNE, the lowest one is found for CTC formed by imidazolidine-2-thione. Molecular associate formed by pyridine-2-thione and TCNE has the greatest stability in the chloroform solution. 5-Trifluoromethylpyridine-2-thione and 4-trifluoromethylpyrimidine-2-thione do not form CTC in CH3CN due to the presence of an electron acceptor group in the molecules. The molar extinction values of CTC vary within the range of 0.4 × 103 to 1.0 × 104 M-1 cm-1. An analytical strategy of thioamides identification based on wavelength and intensity of CTCs absorption band has been suggested.

Thiol-induced nitric oxide donation mechanisms in substituted dinitrobenzofuroxans.

The goal of present work is the quantum chemical study of NO donation mechanism in dinitrobenzofuroxan aryl derivative. Mechanisms of its structural non-rigidity (1,3-N-oxidic and Boulton-Katritzky rearrangements) and minimum energy pathways of NO donation under the action of sulfanyl radical SH· were considered in details. DFT calculations were performed using B3LYP and UB3LYP functionals in the 6-311++G(d,p) basis set. Obtained results showed that a high experimentally proven NO-donor activity of dinitrobenzofuroxan aryl derivative is connected with its existence in the form of mixture of 1-N-oxide and 3-N-oxide, where the 3-N-oxide is more reactive towards SH·. The thiol-induced low-barrier mechanism of NO-donation is a result of para-aminophenyl substituent availability in position 7 of dinitrobenzofuroxan.

2-alpha-hydroxyalkyl- and 2,7-di(alpha-hydroxyalkyl)-1,8-bis(dimethylamino)naphthalenes: stabilization of nonconventional in/out conformers of "proton sponges" via N...H-O intramolecular hydrogen bonding. A remarkable kind of tandem nitrogen inversion.

A regular set of 2-(alpha-hydroxymethyl)- and 2,7-di(alpha-hydroxymethyl)-1,8-bis(dimethylamino)naphthalenes has been prepared. Their X-ray, NMR, and IR studies have demonstrated that in tertiary mono-alcohols the orientation of free nitrogen electron pairs in crystals and solution corresponds to nonconventional in/out conformers stabilized by O-H...N intramolecular hydrogen bonding. For tertiary 2,7-dialcohols, the superimposed equilibrating in/out-out/in nitrogen invertomers are observed in solution. Unlike this, primary and secondary mono- and dialcohols commonly exist in the in/in form, which is typical for the parent proton sponge and the majority of its derivatives.