Identification of allosteric hotspots regulating the ribosomal RNA binding by antibiotic resistance-conferring Erm methyltransferases.

Antibiotic resistance via epigenetic methylation of ribosomal RNA is one of the most prevalent strategies adopted by multidrug resistant pathogens. The erythromycin-resistance methyltransferase (Erm) methylates rRNA at the conserved A2058 position and imparts resistance to macrolides such as erythromycin. However, the precise mechanism adopted by Erm methyltransferases for locating the target base within a complicated rRNA scaffold remains unclear. Here, we show that a conserved RNA architecture, including specific bulge sites, present more than 15 Å from the reaction center, is key to methylation at the pathogenic site. Using a set of RNA sequences site-specifically labeled by fluorescent nucleotide surrogates, we show that base flipping is a prerequisite for effective methylation and that distal bases assist in the recognition and flipping at the reaction center. The Erm-RNA complex model revealed that intrinsically flipped-out bases in the RNA serve as a putative anchor point for the Erm. Molecular dynamic simulation studies demonstrated the RNA undergoes a substantial change in conformation to facilitate an effective protein-rRNA handshake. This study highlights the importance of unique architectural features exploited by RNA to impart fidelity to RNA methyltransferases via enabling allosteric crosstalk. Moreover, the distal trigger sites identified here serve as attractive hotspots for the development of combination drug therapy aimed at reversing resistance.

Expanding the Horizon of Bio-Inspired Catalyst Design with Tactical Incorporation of Drug Molecules.

The development of potent H2 production catalysts is a key aspect in our journey toward the establishment of a sustainable carbon-neutral power infrastructure. Hydrogenase enzymes provide the blueprint for designing efficient catalysts by the rational combination of central metal core and protein scaffold-based outer coordination sphere (OCS). Traditionally, a biomimetic catalyst is crafted by including natural amino acids as OCS features around a synthetic metal motif to functionally imitate the metalloenzyme activity. Here, we have pursued an unconventional approach and implanted two distinct drug molecules (isoniazid and nicotine hydrazide) at the axial position of a cobalt core to create a new genre of synthetic catalysts. The resultant cobalt complexes are active for both electrocatalytic and photocatalytic H2 production in near-neutral water, where they significantly enhance the catalytic performance of the unfunctionalized parent cobalt complex. The drug molecules showcased a dual effect as they influence the catalytic HER by improving the surrounding proton relay along and exerting subtle electronic effects. The isoniazid-ligated catalyst C1 outperformed the nicotine hydrazide-bound complex C2, as it produced H2 from water (pH 6.0) at a rate of 3960 s-1 while exhibiting Faradaic efficiency of about 90 %. This strategy opens up newer avenues of bio-inspired catalyst design beyond amino acid-based OCS features.

Photodegradation of Flutamide and Halogen Derivatives of Nitrobenzotrifluoride: The NO Release Channel.

The photodegradation of the nonsteroidal antiandrogen drug flutamide has been long linked to the photoisomerization involving the nitro group. In this work, the dynamics of NO photoelimination upon photolysis at 266 nm of flutamide, nitrobenzotrifluoride, and its halogen derivatives were investigated. Similar to nitrobenzene and its derivatives, a bimodal translational energy distribution was observed for the NO photofragment indicating the presence of two distinct elimination channels resulting in slow and fast components. The trends in the slow/fast branching ratio show that halogen substitution at the para position increases the triplet state yield due to the internal heavy-atom effect leading to enhancement of the fast component. Furthermore, the topology of the triplet state potential energy surface showed that the minimum energy path favors the oxaziridine ring-type intermediate over the NO2 roaming mechanism in all five molecules investigated. The steric interaction between the NO2 group and the CF3 group, which are placed in the ortho position, lowers the barrier for the formation of the oxaziridine transition state compared to that of nitrobenzene.

Ab initio anharmonic analysis of complex vibrational spectra of phenylacetylene and fluorophenylacetylenes in the acetylenic and aromatic C-H stretching region.

Vibrational spectra in the acetylenic and aromatic C-H stretching regions of phenylacetylene and fluorophenylacetylenes, viz., 2-fluorophenylacetylene, 3-fluorophenylacetylene, and 4-fluorophenylacetylene, were measured using the IR-UV double resonance spectroscopic method. The spectra, in both acetylenic and aromatic C-H stretching regions, were complex exhibiting multiple bands. Ab-initio anharmonic calculations with quartic potential using B97D3/6-311++G(d,p) and vibrational configuration interaction were able to capture all important spectral features in both the regions of the experimentally observed spectra for all four molecules considered in the present work. Interestingly, for phenylacetylene, the spectrum in the acetylenic C-H stretching region emerges due to anharmonic coupling of modes localized on the acetylenic moiety along with the other ring modes, which also involve displacements on the acetylenic group, which is in contrast to what has been proposed and propagated in the literature. In general, this coupling scheme is invariant to the fluorine atom substitution. For the aromatic C-H stretching region, the observed spectrum emerges due to the coupling of the C-H stretching with C-C stretching and C-H in-plane bending modes.

Binary Matrix Method to Enumerate, Hierarchically Order, and Structurally Classify Peptide Aggregation.

Protein aggregation is a common and complex phenomenon in biological processes, yet a robust analysis of this aggregation process remains elusive. The commonly used methods such as center-of-mass to center-of-mass (COM-COM) distance, the radius of gyration (Rg), hydrogen bonding (HB), and solvent accessible surface area do not quantify the aggregation accurately. Herein, a new and robust method that uses an aggregation matrix (AM) approach to investigate peptide aggregation in a MD simulation trajectory is presented. An nxn two-dimensional AM is created by using the interpeptide Cα-Cα cutoff distances, which are binarily encoded (0 or 1). These aggregation matrices are analyzed to enumerate, hierarchically order, and structurally classify the aggregates. Comparison of the present AM method suggests that it is superior to the HB method since it can incorporate nonspecific interactions and the Rg and COM-COM methods since the cutoff distance is independent of the length of the peptide. More importantly, the present method can structurally classify the peptide aggregates, which the conventional Rg, COM-COM, and HB methods fail to do. The unique selling point of this method is its ability to structurally classify peptide aggregates using two-dimensional matrices.

Vibrational Stark fields in carboxylic acid dimers.

Carboxylic acids form exceptionally stable dimers and have been used to model proton and double proton transfer processes. The stabilization energies of the carboxylic acid dimers are very weakly dependent on the nature of substitution. However, the electric field experienced by the OH group of a particular carboxylic acid is dependent more on the nature of the substitution on the dimer partner. In general, the electric field was higher when the partner was substituted with an electron-donating group and lower with an electron-withdrawing substituent on the partner. The Stark tuning rate (Δ) of the O-H stretching vibrations calculated at the MP2/aug-cc-pVDZ level was found to be weakly dependent on the nature of substitution on the carboxylic acid. The average Stark tuning rate of O-H stretching vibrations of a particular carboxylic acid when paired with other acids was 5.7 cm-1 (MV cm-1)-1, while the corresponding average Stark tuning rate of the partner acids due to a particular carboxylic acid was 21.9 cm-1 (MV cm-1)-1. The difference in the Stark tuning rate is attributed to the primary and secondary effects of substitution on the carboxylic acid. The average Stark tuning rate for the anharmonic O-D frequency shifts is about 40-50% higher than the corresponding harmonic O-D frequency shifts calculated at the B3LYP/aug-cc-pVDZ level, much greater than the typical scaling factors used, indicating the strong anharmonicity of O-H/O-D oscillators in carboxylic acid dimers. Finally, the linear correlation observed between pKa and the electric field was used to estimate the pKa of fluoroformic acid to be around 0.9.

Dynamics of Methyl Radical Formation Following 266 nm Dissociative Photoionization of Xylenes and Mesitylene.

The 266 nm dissociative photoionization of three xylene isomers and mesitylene leading to the formation of methyl radical was examined. The total translational energy distribution profiles [P(ET)] for the methyl radical were almost identical for all of the three isomers of xylene and mesitylene, while a substantial difference was observed for the corresponding P(ET) profile of the co-fragment produced by loss of one methyl group in m-xylene. This observation is attributed to the formation of the methyl radical from alternate channels induced by the probe. The P(ET) profiles were rationalized based on the dissociation of {sp2}C-C{sp3} bond in the cationic state, wherein the {sp2}C-C{sp3} bond dissociation energy is substantially lower relative to the neutral ground state. The dissociation in the cationic state follows a resonant three-photon absorption process, resulting in a maximum translational energy of about 1.6-1.8 eV for the photofragments in the center-of-mass frame. Fitting of the P(ET) profiles to empirical function reveals that the dynamics of {sp2}C-C{sp3} bond dissociation is insensitive to the position of substitution but marginally dependent on the number of methyl groups.

Dipole moment enhanced π-π stacking in fluorophenylacetylenes is carried over from gas-phase dimers to crystal structures propagated through liquid like clusters.

The aggregates of monofluorinated phenylacetylenes in the gas-phase, investigated using the IR-UV double resonance spectroscopic method in combination with extensive structural search and electronic structure calculations, reveal the formation of liquid-like clusters with a π-stacked dimeric core. The structural assignment based on the IR spectra in the acetylenic and aromatic C-H stretching regions suggests that, unlike the parent non-fluorinated phenylacetylene, the substitution of a F atom on the phenyl ring increases the dipole moment, leading to robustness in the formation of a ππ stacked dimer, which propagates incorporating C-Hπ_{Ar/Ac} and C-HF interactions involving both acetylenic and aromatic C-H groups. The structural evolution of fluorophenylacetylene aggregates in the gas phase shows marginal effects due to fluorine atom position on the phenyl ring, with substitution in the para-position tending towards phenylacetylene. The present study signifies that the ππ stacked dimers act as a nucleus for the growth of higher clusters to which other molecular units are added predominantly via the {Ar}_C-Hπ_{Ar} type of interaction and the dominant interactions present in the crystal structures gradually emerge with increasing cluster size. Based on these features, gas-phase clusters of fluorophenylacetylene are hypothesized as "liquid-like clusters" acting as intermediates in the generation of various polymorphic forms starting from a ππ stacked dimer as the core molecular unit.

Understanding Fermi resonances in the complex vibrational spectra of the methyl groups in methylamines.

Vibrational spectra of the methyl groups in mono-methylamine (MMA), dimethylamine (DMA), and trimethylamine (TMA) monomers and their clusters were measured in three experimental set-ups to capture their complex spectral features as a result of bend/umbrella-stretch Fermi resonance (FR). Multiple bands were observed between 2800 and 3000 cm-1 corresponding to the methyl groups for MMA and DMA. On the other hand, the corresponding spectrum of TMA is relatively simple, exhibiting only four prominent bands in the same frequency window, even though TMA has a larger number of methyl groups. The discrete variable representation (DVR) based ab initio anharmonic algorithm with potential energy surface (PES) at CCSD/aug-cc-pVDZ quality is able to capture all the experimentally observed spectral features across all three amines, and the constructed vibrational Hamiltonian was used to analyze the couplings that give rise to the observed FR patterns. It was observed that the vibrational coupling among CH stretch modes on different methyl groups is weak (less than 2 cm-1) and stronger vibrational coupling is found to localize within a methyl group. In MMA and DMA, the complex feature between 2850 and 2950 cm-1 is a consequence of closely packed overtone states that gain intensities by mixing with the stretching modes. The simplification of the spectral pattern of TMA can be understood by the red-shift of the symmetric CH3 stretching modes by about 80 cm-1 relative to MMA, which causes the symmetric CH3 stretch to shift outside the FR window.

Is Dissociation of HCl in DMSO Clusters Bistable?

Dissociation of HCl embedded in dimethyl sulfoxide (DMSO) clusters was investigated by projecting the solvent electric field along the HCl bond using B3LYP-D3/6-31+G(d) and MP2/6-31+G(d,p) levels of theory. A large number of distinct structures (about 1500) consisting of up to five DMSO molecules were considered in the present work for statistical reliability. The B3LYP-D3 calculations reveal that the dissociation of HCl embedded in DMSO clusters requires a critical electric field of 138 MV cm-1 along the H-Cl bond. However, a large number of exceptions wherein the electric field values much higher than the critical electric field of 138 MV cm-1 did not result in dissociation of HCl were observed, in addition to several cases wherein the HCl dissociates with an electric field less than the critical electric field. On the other hand, the MP2 level calculations reveal that the critical electric field for HCl dissociation is about 181 MV cm-1 with almost no exceptions. A comparison of calculations carried out using the MP2 and the B3LYP-D3 levels suggests that the dissociation of HCl embedded in DMSO clusters is bistable at the B3LYP-D3 level, which is an artifact, suggesting that care must be exercised in interpreting the processes of proton transfer. The answer to the question raised as the title of this paper is NO.

Hydrogen-Bonded Complexes of Fluorophenylacetylenes: To Fluoresce or Not?

The hydrogen-bonded complexes of fluorophenylacetylenesexhibit unusual and interesting fluorescence turn ON/OFF behaviour following excitation to 1 ππ* (S1 ) state. The fluorescence switching behaviour can be realized by (i) "change in the intermolecular structure, (ii) change in the position of fluorine substitution and (iii) change in the hydrogen bonding partner or a combination thereof. Experiments indicate that the ≡C-H⋅⋅⋅X (X=O, N) hydrogen bonding with the acetylenic group plays a pivotal role in this switching behaviour. Intriguingly, weaker ≡C-H⋅⋅⋅X hydrogen bonding leads to fluorescence OFF state, which is turned ON by stronger hydrogen bonding. The observed fluorescence this switching behaviour is rationalized on the basis of a phenomenological model which suggests a coupling between the initially excited S1 state and a dark Sn state in the Franck-Condon region with limited window controlled by the ≡C-H⋅⋅⋅X hydrogen bonding as a crucial parameter. Such fluorescence switching behaviour in hydrogen-bonded complexes is unprecedented and these intriguing results hopefully will stimulate theoreticians to test 'state of the art' theories to explain these observations in a consistent manner.

Internal electric fields in methanol [MeOH]2-6 clusters.

Water and methanol are well known solvents showing cooperative hydrogen bonding, however the differences in the hydrogen bonding pattern in water and methanol are due to the presence of the methyl group in methanol. The presence of the methyl group leads to formation of C-HO hydrogen bonds apart from the usual O-HO hydrogen bonds. The electric fields evaluated along the hydrogen bonded donor OH and CH groups reveal that the C-HO hydrogen bonds can significantly influence the structure and energetics (by about 20%) of methanol clusters. A linear Stark effect was observed on the hydrogen bonded OH groups in methanol clusters with a Stark tuning rate of 3.1 cm-1 (MV cm-1)-1 as an average behaviour. Furthermore, the Stark tuning of the OH oscillators in methanol depends on their hydrogen bonding environment wherein molecules with the DAA motif show higher rates than the rest. The present work suggests that the OH group of methanol has higher sensitivity as a vibrational probe relative to the OH group of water.

Dipole Moment Propels π-Stacking of Heterodimers of Fluorophenylacetylenes.

Electronic and vibrational spectroscopic investigations in combination with quantum chemical calculations were carried out to probe the formation of four sets of heterodimers of phenylacetylene with 2-fluorohenylacetylene, 3-fluorophenylacetylene, 4-fluorophenylacetylene, and 2,6-difluorophenylacetylene. The interaction of phenylacetylene with fluorophenylacetylenes leads to marginal (2-9 cm-1) red-shifts in the acetylenic C-H stretching frequencies of fluorophenylacetylenes, which suggests that constituent monomers are minimally perturbed in the heterodimer. On the other hand, the density-functional-theory-based calculations indicate that π-stacked structures outweigh other structures incorporating C-H···π and C-H···F interactions by about 8 kJ mol-1 or more. The IR spectra in the acetylenic C-H stretching region were interpreted based on the perturbed dipole model, which suggests formation of predominantly antiparallel π-stacked structures, propelled by dipole moment. However, the energy decomposition analysis suggests that among stabilizing components dispersion dominates, while electrostatics plays a pivotal role in the formation of the π-stacked structures. Interestingly, the ability of 2-fluorophenylacetylene and 2,6-difluorophenylacetylene to π-stack differs significantly, even though both of them have almost identical dipole moments and the dipole moment propels the formation of π-stack structures. These results suggest π-stacking transcends the classical electrostatic description in terms of dipole moment.

Bend-to-Break: Curvilinear Proton Transfer in Phenol-Ammonia Clusters.

The electric field experienced by the OH group of phenol embedded in the cluster of ammonia molecules depends on the relative orientation of the ammonia molecules, and a critical field of 236 MV cm-1 is essential for the transfer of a proton from phenol to the surrounding ammonia cluster. However, exceptions to this rule were observed, which indicates that the projection of the solvent electric field over the O-H bond is not a definite descriptor of the proton transfer reaction. Therefore, a critical electric field is necessary, but it is not a sufficient condition for the proton abstraction. This, in combination with an adequate solvation of the acceptor ammonia molecule in a triple donor motif that energetically favors the proton transfer process, constitutes necessary and sufficient conditions for the spontaneous proton abstraction. The proton transfer process in phenol-(ammonia)n clusters is statistically favored to occur away from the plane of the phenyl ring and follows a curvilinear path which includes the O-H bond elongation and out-of-plane movement of the proton. Colloquially, this proton transfer can be referred to as a "bend-to-break" process.

π-Stacking Driven Aggregation and Folding of Squaramides.

Competing noncovalent interactions play a pivotal role in the folding and assembly of three-dimensional structures, especially in flexible molecules. Calculations using density functional theory reveal that two squaramide rings aggregate to form a slipped antiparallel π-stacked dimer with high propensity. This π-π stacking interaction is used to design foldamers in which the squaramides are tethered by a simple methylene bridge, and consequently, the structure folds on to itself incorporating a "turn" element. The variation in relative energy with respect to change in dihedral angle for these foldamers show that for all the structures two rings are displaced in space and the folding potential is asymmetric, starting from seemingly symmetric molecules. The addition of successive squaramide rings connected with simple methylene bridges leads to the formation of higher-order structures with a "Turn-Stack-Turn" structural motif. The "Turn-Stack-Turn" motif can be used in designing new synthetic foldamers which could potentially mimic closely related biological systems. Further, it was found that the aggregation of the folded structures was energetically favored over the unfolded structures. The present set of calculations are important in light of the fact that these simple methylene bridged squaramide rings present synthetic challenges.

Vibrational spectroscopic signatures of hydrogen bond induced NH stretch-bend Fermi-resonance in amines: The methylamine clusters and other N-H⋯N hydrogen-bonded complexes.

The appearance of multiple bands in the N-H stretching region of the infrared spectra of the neutral methylamine dimer and trimer is a sign of NH bend-stretch anharmonic coupling. Ab initio anharmonic calculations were carried out in a step-wise manner to reveal the origin of various bands observed in the spectrum of the methylamine dimer. A seven-dimensional potential energy surface involving symmetric and asymmetric stretching and bending vibrations of both the hydrogen bond donor and the acceptor along intermolecular-translational modes was constructed using the discrete variable representation approach. The resulting spectrum of the dimer shows five bands that can be attributed to the symmetric stretching (νsym D), asymmetric stretchin (νasym D), and bending overtone (2νbend D) of the donor moiety. These appear along with the combination band arising out of bending vibrations of the donor and acceptor (νbend D + νbend A) and with the combination of the intermolecular translational mode over the donor bending overtone (νtrans + 2νbend D). The spectrum of the trimer essentially consists of all the features seen in the dimer with marginal changes in band positions. The analysis of the experimental spectra based on the two-state deperturbation model and ab initio anharmonic calculations yield a matrix element of about 40 cm-1 for the N-H bend-stretch Fermi resonance coupling. In general, the IR spectra of the hydrogen-bonded amino group depict three sets of bands that arise due to bend-stretch Fermi resonance coupling.

Probing the role of dispersion energy on structural transformation of double-stranded xylo- and ribo-nucleic acids.

The structural transformation of double-stranded octameric xyloNA and RNA were probed by modulating the dispersion energy. For the RNA, the increase and the decrease in dispersion energy lead to over-winding and unwinding of the helix. These structural transformations resemble the features observed due to the action of the topoisomerases and helicases enzymes, respectively. On the other hand, an increase in the dispersion energy has minimal effect on the structural transformation of double-strand xyloNA, whilst a decrease in the dispersion energy results in a structural transformation which happens due to the action of the helicases. The unresponsive behaviour of xyloNA to an increase in the dispersion energy is attributed to the presence of an Lpπ interaction between the oxygen atom of the xylose sugar and the adjacent nucleobase.

A liquid crucible model for aggregation of phenylacetylene in the gas phase.

The aggregation of phenylacetylene in the gas phase was investigated by selectively recording the IR spectra of clusters consisting of up to six monomer units. Analysis of the IR spectra with the aid of B97-D3/aug-cc-pVDZ level calculations reveals the formation of an anti-parallel π-stacked structure of the dimer and a hitherto unknown assembly of clusters incorporating exclusively aromatic C-Hπ interactions between various units of the trimer and higher clusters. The aggregation behaviour of phenylacetylene in the gas phase is fundamentally different from benzene, phenol and aniline vis-à-vis their crystal structures. The structures of the three known polymorphic crystals can be reconciled by the formation of supramolecular synthons with acetylenic C-Hπ interactions, which is preferred over energetically favored aromatic C-Hπ interactions. Furthermore, the small (phenylacetylene)n [n = 3-6] clusters, the structures incorporating aromatic C-Hπ interactions, can be envisaged as liquid-like aggregates which under varied conditions lead to the formation of multiple polymorphs during in situ cryo-crystallization.

Hydrogen bond induced enhancement of Fermi resonances in N-HN hydrogen bonded complexes of anilines.

The hydrogen-bonded complexes of aniline, 4-fluoroaniline and 4-ethynylaniline with ammonia, methylamine, dimethylamine, trimethylamine and triethylamine, were investigated using IR-UV double resonance spectroscopy. The formation of N-HN hydrogen bonded complexes with anilines as donors and alkylamines as acceptors was inferred from the appearance of the spectra. Two bands appearing in the 3100-3400 cm-1 region were found to be originating from the Fermi resonance coupling between the hydrogen-bonded NH2 stretching and NH2 bend-overtone vibrations. A two-state de-perturbation analysis yields the zero-order (unperturbed) vibrational states and the coupling constant. An inverse correlation between the zero-order hydrogen-bonded NH2 stretching and NH2 bend-overtone was observed due to a switch in the relative contributions of hydrogen-bonded NH2 stretching and NH2 bend-overtone vibrations to the Fermi resonance bands. These results lead to the reassignment of the hydrogen-bonded N-H stretching frequencies of aniline complexes reported earlier. Furthermore, the stretch-bend Fermi-resonance coupling constant for the NH2 group is around 50 cm-1, which is independent of the nature of the parent donor molecule and the acceptor, and is intrinsic to the NH2 group.

The role of electronegativity on the extent of nitridation of group 5 metals as revealed by reactions of tantalum cluster cations with ammonia molecules.

Reactions of the free tantalum cation, Ta+, and tantalum cluster cations, Tan+ (n = 2-10), with ammonia are presented. The reaction of the monomer cation, Ta+, with two molecules of NH3 leads to the formation of TaN2H2+ along with release of two H2 molecules. The dehydrogenation occurs until the formal oxidation number of the tantalum atom reaches +5. On the other hand, all the tantalum cluster cations, Tan+, react with two molecules of NH3 and form TanN2+ with the release of three H2 molecules. Further exposure to ammonia showed that TanNmH+ and TanNm+ are produced through successive reactions; a pure nitride and three H2 molecules are formed for every other NH3 molecule. The nitridation occurred until the formal oxidation number of the tantalum atoms reaches +5 as in the case of TaN2H2+ in contrast to other group 5 elements, i.e., vanadium and niobium, which have been reported to produce nitrides with lower oxidation states. The present results on small gas-phase metal-nitride clusters show correlation with their bulk properties: tantalum is known to form bulk nitrides in the oxidation states of either +5 (Ta3N5) or +3 (TaN), whereas vanadium and niobium form nitrides in the oxidation state of +3 (VN and NbN). Along with DFT calculations, these findings reveal that nitridation is driven by the electron-donating ability of group 5 elements, i.e., electronegativity of the metal plays a key role in determining the composition of the metal nitrides.