A novel hydrogen-bonding N-oxide–sulfonamide–nitro N—H...O synthon determining the architecture of benzenesulfonamide cocrystals

The structures of novel cocrystals of 4-nitropyridine N-oxide with benzenesulfonamide derivatives, namely, 4-nitrobenzenesulfonamide–4-nitropyridine N-oxide (1/1), C5H4N2O3·C6H6N2O4S, and 4-chlorobenzenesulfonamide–4-nitropyridine N-oxide (1/1), C6H6ClNO2S·C5H4N2O3, are stabilized by N—H...O hydrogen bonds, with the sulfonamide group acting as a proton donor. The O atoms of the N-oxide and nitro groups are acceptors in these interactions. The latter is a double acceptor of bifurcated hydrogen bonds. Previous studies on similar crystal structures indicated competition between these functional groups in the formation of hydrogen bonds, with the priority being for the N-oxide group. In contrast, the present X-ray studies indicate the existence of a hydrogen-bonding synthon including N—H...O(N-oxide) and N—H...O(nitro) bridges. We present here a more detailed analysis of the N-oxide–sulfonamide–nitro N—H...O ternary complex with quantum theory computations and the Quantum Theory of Atoms in Molecules (QTAIM) approach. Both interactions are present in the crystals, but the O atom of the N-oxide group is found to be a more effective proton acceptor in hydrogen bonds, with an interaction energy about twice that of the nitro-group O atoms.

Quantum Surprises from the Watson-Crick and Hoogsteen G·C Nucleobase Pairs: A Comprehensive QM/QTAIM Investigation

In this study at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory in the isolated state it was revealed 14 novel physico-chemical mechanisms of the tautomerization of the G·C nucleotide base pairs in the Watson-Crick G·C(WC) / G*·C*(WC), reverse Watson-Crick G*·C*(rWC) / G·C*O2(rWC), Hoogsteen G*t·C*(H) / G*N7·C(H) or reverse Hoogsteen G*t·C*(rH) / G*tN7·C(rH) configurations into the wobble (wWC, wH) and reverse wobble (rwWC, rwН) base pairs: 1. G·C(WC)↔G·C*(rwWC), 2./3. G*·C*(WC)↔G·C*(rwWC)/G*N2·C*(rwWC), 4. G*·C*(rWC)↔G*·C(wWC), 5. G·C*O2(rWC)↔G·C*(wWC); 6./7./8./9. G*t·C*(H)↔G*t·C(rwН)/G*t·C*O2(wH)/G*t·C*O2(rwН)/G*tN7·C*(rwН)↔G*t·C*O2(rwН), 10. G*N7·C(H)↔G*t·C(wH) amino, 11./12. G*t·C*(rH)↔G*N7·C*(wН)/G*t·C(wН), 13. G*tN7·C(rH)↔G*tN7·C*(wН)↔G*t·C(wН) and 14. G*N7·C*(rwH)↔G*N7·C*(rwH) perp↔G-·C+(wH)↔G*t·C(rwН) reaction pathways. It was established that the presence in the base pair of the two anti-parallel neighboring H-bonds is a necessary and sufficient condition for the implementation of such transformations, since it enables intermolecular proton transfer between the bases inside the base pair. It was found out that these tautomeric transitions are controlled by the TSs with quasi-orthogonal structure, which are tight G+·C-/G-·C+ ion pairs, joined by at least two parallel intermolecular H-bonds, connected on a common negatively charged endocyclic N-/C- atoms – proton acceptor. All reaction pathways have been reliably confirmed. These transitions are accompanied by the changing of the mutual cis-orientation of the N9H and N1H glycosidic bonds of the bases on the trans-orientation and vice versa. These data complement the reported earlier mechanisms of the tautomerisations of the classical A·T and G·C DNA base pairs. Experimental verification of the novel G·C nucleobase pairs is looking as an attractive task for the future research.

An Insight into the Proofreading Functions of Multisubunit DNA-Dependent RNA Polymerases and Their Catalytic Mechanism

Aim: To analyze the active sites of the proofreading (PR) functions in the multisubunit DNA-dependent RNA polymerases (MSU RNAPs) from prokaryotes, chloroplasts and eukaryotes, and propose a plausible unified catalytic mechanism for these enzymes. Study Design: Data collected on these enzymes from bioinformatics, biochemical, site-directed mutagenesis (SDM), X-ray crystallography and cryo-electron microscopy (cryo-EM) were used for the analyses. Methodology: The protein sequence data of MSU RNAPs from prokaryotes, prokaryotic-types (plant chloroplasts) and eukaryotes were obtained from PUBMED and SWISS-PROT databases. The advanced version of Clustal Omega was used for protein sequence analysis. Along with the conserved motifs identified by the bioinformatics analysis, the data already available from biochemical and SDM experiments, and X-ray crystallographic and cryo-EM data on these enzymes are also used to confirm the possible amino acids involved in the active site of the PR function in these MSU RNAPs Results: All the seven types of MSU RNAPs (I-VII) reported from prokaryotes to eukaryotes were analyzed by the multiple sequence alignment (MSA) software, Clustal Omega, to find out conservations among them. The MSA analysis showed many conserved amino acid motifs including small and large peptide regions from the MSU RNAPs of prokaryotes, eukaryotes and plant chloroplasts. Interestingly, the catalytic amino acid and template-binding pairs are highly conserved in all these polymerases, with a few exceptions. Most of them use a basic amino acid (R/K/H) for initiating catalysis and an -YG/FG- pair for template-binding. Some odd type of catalytic amino acids and template-binding pairs are observed in human pathogens, parasites and organisms which cannot ferment sugars. In all the MSU RNAPs, the proposed polymerase catalytic region also possessed three invariant Cs and an invariant H within it. The invariant Cs is shown to bind a zinc atom and proposed to involve in the PR function by excising any misincorporated nucleotide during the transcription process. In the plant-specific MSU RNAPs IV and V, which involve in transcriptional gene silencing in plants, the catalytic and template-binding pairs do not follow the regular distance conservations as observed with other five of the MSU RNAPs. Their polymerase/PR active site regions are similar to RNAP III rather than to RNAP II, as all three make only low molecular weight RNAs. Conclusions: All the known MSU RNAPs possess three invariant Cs and an invariant H embedded within the polymerase active site itself. The three invariant Cs are shown to bind a zinc atom and the invariant H could act as the proton acceptor from a metal-bound water molecule, for initiating excision of the mismatches by a Zn-mediated hydrolysis. Thus, the PR function in MSU RNAPs is integrated within the polymerase active site itself, which is in sharp contrast to the PR functions reported in DNA-dependent DNA polymerases and RNA-dependent RNA polymerases. Therefore, all the seven MSU RNAPs from prokaryotes and eukaryotes are proposed to follow a unified mechanism to excise the mismatches during transcription. The discovery of intrinsic self-correcting RNA transcription mechanism fulfils the missing link in molecular evolution.

Intelligent Numerical Computing Methods for Determining the Concentration of Citric Acid by Accurate Measurement and Calculation

According to the Bronsted-Lowry theory, an acid is a proton donor, and a base is a proton acceptor. An acid-base reaction involves the proton transfer between chemicals, where a base containing hydroxide ion (OH-) accepts a proton (H+) from an acidic solution to form water (Khan,2016). In the above equation, HCl as an acid donates one H+ ion, and NaOH as a base accepts the proton to form one water molecule (H2O). So, a proton from the acid is transferred to the anion of the base. Then, the metal cation (Na+) and the conjugate base anion (Cl-) form the salt NaCl.

Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 Å: the structural basis for dimerisation

The dimeric reaction centre light-harvesting 1 (RC-LH1) core complex of Rhodobacter sphaeroides converts absorbed light energy to a charge separation, and then it reduces a quinone electron and proton acceptor to a quinol. The angle between the two monomers imposes a bent configuration on the dimer complex, which exerts a major influence on the curvature of the membrane vesicles, known as chromatophores, where the light-driven photosynthetic reactions take place. To investigate the dimerisation interface between two RC-LH1 monomers, we determined the cryogenic electron microscopy structure of the dimeric complex at 2.9 Å resolution. The structure shows that each monomer consists of a central RC partly enclosed by a 14-subunit LH1 ring held in an open state by PufX and protein-Y polypeptides, thus enabling quinones to enter and leave the complex. Two monomers are brought together through N-terminal interactions between PufX polypeptides on the cytoplasmic side of the complex, augmented by two novel transmembrane polypeptides, designated protein-Z, that bind to the outer faces of the two central LH1 β polypeptides. The precise fit at the dimer interface, enabled by PufX and protein-Z, by C-terminal interactions between opposing LH1 αβ subunits, and by a series of interactions with a bound sulfoquinovosyl diacylglycerol lipid, bring together each monomer creating an S-shaped array of 28 bacteriochlorophylls. The seamless join between the two sets of LH1 bacteriochlorophylls provides a path for excitation energy absorbed by one half of the complex to migrate across the dimer interface to the other half.

Insights into the Mechanism of an Allylic Arylation Reaction via Photoredox Coupled Hydrogen Atom Transfer

Despite widespread use as a synthetic method, as well as rapid expansion of substrate scope, the precise mechanism and kinetics of photoredox coupled hydrogen atom transfer (HAT) reactions remain poorly understood. This results from a lack of detailed kinetic information, as well as the identification of side reactions and products. In this report, a mechanistic study of a prototypical tandem photoredox/HAT reaction coupling cyclohexene and 1,4-Dicyanobenzene (DCB) using an Ir(ppy)3 photocatalyst and thiol HAT catalyst is reported. Through a combination of electrochemical, photochemical, and spectroscopic measurements, key unproductive pathways and side products are identified and rate constants for main chemical steps are extracted. The reaction quantum yield was found to decline rapidly over the course of the 20-hour reaction. A previously unreported cyanohydrin side product was identified and thought to play a key role as proton acceptor in the reaction. Transient absorption spectroscopy (TAS) suggested a reaction mechanism that involves trapping of the DCB radical anion by cyclohexene with HAT occurring as the final step via a cooperative HAT step. Kinetic modeling of the reaction, using rate constants derived from TAS, demonstrates that the efficiency of the reaction is limited by parasitic absorption and unproductive quenching between excited Ir(ppy)3 and the cyanohydrin photoproduct.

An Overview of the Proofreading Functions in Bacteria and in Severe Acute Respiratory Syndrome-Coronaviruses

Aim: To understand the structure-function relationship of the proofreading (PR) functions in eubacteria and viruses with special reference to Severe Acute Respiratory Syndrome-Coronaviruses (SARS-CoVs) and propose a plausible mechanism of action for PR exonucleases of SARS-CoVs. Study Design: Bioinformatics, biochemical, site-directed mutagenesis (SDM), X-ray crystallographic data were used to study the structure-function relationships of the PR exonucleases from bacteria and CoVs. Methodology: The protein sequences of the PR exonucleases of various DNA polymerases, and RNA polymerases of SARS, SARS-related and human CoVs (HCoVs) were obtained from PUBMED and SWISS-PROT databases. The advanced version of Clustal Omega was used for protein sequence analysis. Along with the conserved motifs identified by the bioinformatics analysis, the data already available by biochemical, SDM experiments and X-ray crystallographic analysis on these enzymes were used to arrive at the possible active amino acids in the PR exonucleases of these crucial enzymes. Results: A complete analysis of the active sites of the PR exonucleases from various bacteria and CoVs were done. The multiple sequence alignment (MSA) analysis showed many conserved amino acids, small and large peptide regions among them. Based on the conserved motifs, the PR exonucleases are found to fit broadly into two superfamilies, viz. DEDD and polymerase-histidinol phosphatase (PHP) superfamilies. The bacterial DNA polymerases I and II, RNase D, RNase T and ε-subunit of DNA polymerases III belong to the DEDD superfamily. The PR enzymes from SARS, SARS-related CoVs and other HCoVs also essentially belong to the DEDD superfamily. The DEDD superfamily either uses an invariant Tyr or a His as proton acceptor during catalysis. Depending on the proton acceptor, they are further classified into DEDHD and DEDYD subfamilies. RNase T, ε-subunit of DNA polymerases III and the SARS, SARS-related CoVs and other HCoVs belong to DEDHD subfamily. However, the SARS, SARS-related CoVs and other HCoVs showed additional zinc finger motifs (ZFMs) in their active sites. DNA polymerases I, II and RNase D belong to DEDYD subfamily. The bacterial DNA polymerases X, YcdX phosphoesterases and the co-editing exonuclease of DNA polymerases III belong to the PHP superfamily. Based on the MSA, X-ray crystallographic analyses and SDM experiments, the proposed active-site proton acceptor is Tyr/His in DEDDY/H subfamilies and His in PHP superfamily of PR exonucleases. Conclusions: Based on the similarities of active site amino acids/motifs, it may be concluded that the DEDD and PHP superfamilies of PR exonucleases should have evolved from a common ancestor but diverged very long ago. The biochemical properties of these enzymes, including the four conserved acidic amino acid residues in the catalytic core, suggest that the CoVs might have acquired the exonuclease function, possibly from a prokaryote. However, the presence of two zinc fingers in the PR active site of the SARS, SARS-related CoVs and other HCoVs sets their PR exonucleases apart from other homologues.

SPECIFIC NATURE OF ACID-BASE INTERACTION OF OCTA(4-TERT-BUTYLPHENYL)TETRAPYRAZINOPORPHYRAZINE WITH ORGANIC PROTON-ACCEPTOR MOLECULES IN BENZENE

The reaction of acid-base interaction of octa(4-tert-butylphenyl)tetrapyrazinophosphyrazine with pyridine, 2-methylpyridine, morhpoline, pipyridine, n-butylamine, tert-butylamine, diethylamine, triethylamine and dimethylsulfoxide in benzene was investigated. It is shown that the researched porphyrazine forms kinetically stable proton transfer complexes with pyridine, 2-methylpyridine, morpholine and dimethylsulfoxide. In benzene-base system an acid-base equilibrium between the molecular form of octa(4-tert-butylphenyl)tetrapyrazinoporphyrazine and its proton transfer complex was established. The interaction of substituted tetrapyrazinoporphyrazine with morpholine in benzene was revealed to be a kinetically controllable process which occurs with low reaction rate and high values of activation energy. Such values are not inherent to most of relatively simple liquid-phase acid-base systems. The kinetic equation of the process was found, and, based on the spectral changes accompanying the reaction, a cheme of two-stage process of proton transfer of NH-groups of octa(4-tert-butylphenyl)tetrapyrazinoporphyrazine to morpholine in benzene was proposed. A possible structure of proton transfer complex of octa(4-tert-butylphenyl)tetrapyrazinoporphyrazine with organic bases is shown. In these complexes the inner hydrogen atoms of the cycle, bonded with base molecules, lie under and above the plane of the molecule, and the proton transfer from acid to base is limited either by the H-complex or the ion-ion associates constituting an H-bonded ion pair. Depending on the proton accepting tendency of the base, the acid-base equilibrium can shift towards or away from the more or less polarized structure. It was revealed that in benzene - n-butylamine (tri-butylamine, diethylamine, triethylamine, pipyridine) system the acid-base interaction involving octa(4- tert-butylphenyl)tetrapyrazinoporphyrazine occurs incredibly fast, with rates not measurable by standard spectrophotography methods. The forming proton transfer complexes are highly labile due to concurrent proton reaction occurring, leading to the formation of dianion form of octa(4- tert-butylphenyl)tetrapyrazinoporphyrazine. This form undergoes spontaneous dissolution into low-molecular colorless products due to the lack of compensation of excess charge in the macrocycle.