Machine Learned Potential Enables Molecular Dynamics Simulation to Predict the Experimental Branching Ratios in the NO Release Channel of Nitroaromatic Compounds.

This study employs a machine learning (ML) model using the Gaussian process regression algorithm to generate potential energy surfaces (PES) from density functional theory calculations, facilitating the investigation of photodissociation dynamics of nitroaromatic compounds, resulting in NO release. The experimentally observed trends in the slow-to-fast branching ratios of the NO moiety were captured by estimating the branching ratio between the two distinct reaction pathways, viz., roaming and oxaziridine mechanisms, calculated from molecular dynamics simulations performed on a reduced two-dimensional T surface.

Molecular Association and Reactivity of the Pyridine Dimer Cation.

A recent experimental report has identified the formation of the C-N hemibonded pyridine dimer cation following vacuum ultraviolet near-threshold photoionization [, , 12, 4936-4943]. Herein, the dynamics and consequent reactivity of the pyridine dimer cation were investigated employing Born-Oppenheimer molecular dynamics (BOMD) simulations. An antiparallel π-stacked pyridine dimer in the neutral ground state is transformed into a noncovalently interacting C-H···N hydrogen-bonded structure which can lead to proton transfer in the cationic state.

Probing the Role of Solvent Configurations and Local Electric Fields on HX (X = F, Cl, Br and I) Dissociation in Water Clusters.

The acidity of hydrohalic acids increases down the group, with HF and HI being the weakest and strongest acids. Electronic structure calculations suggest that the critical electric fields required for the dissociation of HF, HCl, HBr, and HI are 347, 193, 163, and 153 MV cm, respectively, which are proportional to their corresponding p values and emphasize that in these systems the bond dissociation energy determines the p. The solvent configuration plays a significant role in the acid dissociation process, which is illustrated by a particular configuration of three water molecules around HX and favors dissociation of only HBr, even though the critical electric field required for the dissociation of HI is lower than that of HBr, as depicted in the graphical abstract.

Mechanistic variances in NO release: isomers of nitrophenol and nitroaniline.

The NO release following 266 nm photolysis of and isomers of nitrophenol and nitroaniline shows a bimodal translational energy distribution, wherein the slow and fast components originate from dynamics in the S and T states, respectively. The translational energy distribution profiles for any NO product state show a higher slow-to-fast (s/f) branching ratio for the isomer in comparison with the isomer. The observed variation in the s/f branching ratio the and isomers is attributed to the presence of intramolecular hydrogen bonding between the substituent and NO moiety, which favours the roaming mechanism.

Dissociative Photoionization of Dimethylpyridines and Trimethylpyridine at 266 nm: Dynamics of Methyl Radical Release.

The 266 nm photolysis of various positional isomers of dimethylpyridines and trimethylpyridine was investigated by measuring the translational energy distribution of the methyl radical following {sp}C-C{sp} bond dissociation. The observed translational energy distribution is attributed to the dissociative photoionization in the cationic ground state following [1 + 1 + 1] three-photon absorption. The translational energy distribution profiles of the methyl radical were broad with the maximum translation energy in excess of 2 eV, which originates due to the dissociation of {sp}C-C{sp} bond ortho to the N atom in the ring.

Unraveling the Significance of Mg Dependency and Nucleotide Binding Specificity of H-RAS.

RAS is a small GTPase and acts as a binary molecular switch; the transition from its active to inactive state plays a crucial role in various cell signaling processes. Molecular dynamics simulations at the atomistic level suggest that the absence of cofactor Mg ion generally leads to pronounced structural changes in the than regions and assists GTP binding. The presence of the Mg ion also restricts the rotation of ϒ phosphate and enhances the hydrolysis rate of GTP.

Enticing a Proton using Single Ammonia Molecule as Bait.

In microhydrated acid-solvent clusters, deprotonation of an acid is assisted by a critical number of solvent molecules and a solvent electric field. Born-Oppenheimer molecular dynamics simulations reveal that trifluoroacetic acid undergoes spontaneous proton transfer in water clusters, with the critical number being five. Acetic acid and phenol, on the other hand, do not dissociate even in the presence of a large number of water molecules (in excess of 40).

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.

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.

Dynamics of Hydrogen Bond Breaking Induced by Outer-Valence Intermolecular Coulombic Decay.

The photoexcitation of weakly bound complexes can lead to several decay pathways, depending on the nature of the potential energy surfaces. Upon excitation of a chromophore in a weakly bound complex, ionization of its neighbor upon energy transfer can occur due to a unique relaxation process known as intermolecular Coulombic decay (ICD), a phenomenon of renewed focus owing to its relevance in biological systems. Herein, we report the evidence for outer-valence ICD induced by multiphoton excitation by near-ultraviolet radiation of 4.

Dissociation of Endohedrally Encapsulated HCl/HBr in C and C: An Electric Field Perspective.

The ability of an acid to undergo dissociation depends primarily on the nature of the solvent and especially the arrangement of the solvent molecules around the protic group. This process of acid dissociation can be promoted by confining the solute-solvent system to nanocavities. Endohedral confinement of HCl/HBr complexed with a single ammonia or a water dimer within the C/C cage results in the dissociation of mineral acid.

Modulating the Roaming Dynamics for the NO Release in -Nitrobenzenes.

The dynamics of NO release upon photodissociation of nitroaromatic compounds is dependent on the nature of the interaction between the NO group and substituent in the position. A bimodal (slow and fast) translational energy distribution of the NO photofragment indicates the presence of two distinct NO elimination channels. The slow-to-fast branching ratio for the NO release is regulated by the hydrogen bonding ability of the substituent and follows the order [OH > NH > CH > OCH], indicating that the intramolecular hydrogen bonding plays a pivotal role in NO release dynamics.

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

The development of potent H 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.

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.

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 [()] 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 () profile of the co-fragment produced by loss of one methyl group in -xylene. This observation is attributed to the formation of the methyl radical from alternate channels induced by the probe.

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 (), 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.

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.

Ultrafast Proton-Transfer Reaction in Phenol-(Ammonia) Clusters: An Molecular Dynamics Investigation.

The ability of phenol to transfer a proton to surrounding ammonia molecules in a phenol-(ammonia) cluster depends on the relative orientation of ammonia molecules, and a critical field of about 285 MV cm is essential along the O-H bond for the proton-transfer process. MD simulations reveal that the proton-transfer process from phenol to ammonia cluster is spontaneous when the cluster has at least eight ammonia molecules, and the proton-transfer event is almost instantaneous (about 20-120 fs). These simulations also reveal that the rate-determining step for the proton-transfer process is the reorganization of the solvent around the OH group.

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 along the H-Cl bond.

Π-Stacking in Heterodimers of Propargylbenzene with (Fluoro)phenylacetylenes.

The heterodimers of propargylbenzene (PrBz) with phenylacetylene (PHA) and monosubstituted fluorophenylacetylenes (FPHAs) were investigated using electronic and vibrational spectroscopic methods. The vibrational spectra in the acetylenic C-H stretching region show a marginal shift (0-4 cm) upon dimer formation, which suggests minimal perturbation of the acetylenic group. The M06-2X/aug--pVDZ calculations indicate that the π-stacked structures are the most stable, followed by other structures.

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.

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.

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.

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) 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 or more.

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.