Insights into dietary phytochemicals targeting Parkinson's disease key genes and pathways: A network pharmacology approach.

Parkinson's disease (PD) is a complex neurological disease associated with the degeneration of dopaminergic neurons. Oxidative stress is a key player in instigating apoptosis in dopaminergic neurons. To improve the survival of neurons many dietary phytochemicals have gathered significant attention recently. Thus, the present study implements a comprehensive network pharmacology approach to unravel the mechanisms of action of dietary phytochemicals that benefit disease management. A literature search was performed to identify ligands (i.e., comprising dietary phytochemicals and Food and Drug Administration pre-approved PD drugs) in the PubMed database. Targets associated with selected ligands were extracted from the search tool for interactions of chemicals (STITCH) database. Then, the construction of a gene-gene interaction (GGI) network, analysis of hub-gene, functional and pathway enrichment, associated transcription factors, miRNAs, ligand-target interaction network, docking were performed using various bioinformatics tools together with molecular dynamics (MD) simulations. The database search resulted in 69 ligands and 144 unique targets. GGI and subsequent topological measures indicate histone acetyltransferase p300 (EP300), mitogen-activated protein kinase 1 (MAPK1) or extracellular signal-regulated kinase (ERK)2, and CREB-binding protein (CREBBP) as hub genes. Neurodegeneration, MAPK signaling, apoptosis, and zinc binding are key pathways and gene ontology terms. hsa-miR-5692a and SCNA gene-associated transcription factors interact with all the 3 hub genes. Ligand-target interaction (LTI) network analysis suggest rasagiline and baicalein as candidate ligands targeting MAPK1. Rasagiline and baicalein form stable complexes with the Y205, K330, and V173 residues of MAPK1. Computational molecular insights suggest that baicalein and rasagiline are promising preclinical candidates for PD management.

Advances in Drug Design and Development for Human Therapeutics Using Artificial Intelligence-II.

Building on our 2021-2022 Special Issue, "Advances in Drug Design and Development for Human Therapeutics Using Artificial Intelligence [...].

Advances in Drug Design and Development for Human Therapeutics Using Artificial Intelligence-I.

Artificial intelligence (AI) has emerged as a key player in modern healthcare, especially in the pharmaceutical industry for the development of new drugs and vaccine candidates [...].

Structure-Based Virtual Screening Reveals Ibrutinib and Zanubrutinib as Potential Repurposed Drugs against COVID-19.

Coronavirus disease (COVID)-19 is the leading global health threat to date caused by a severe acute respiratory syndrome coronavirus (SARS-CoV-2). Recent clinical trials reported that the use of Bruton's tyrosine kinase (BTK) inhibitors to treat COVID-19 patients could reduce dyspnea and hypoxia, thromboinflammation, hypercoagulability and improve oxygenation. However, the mechanism of action remains unclear. Thus, this study employs structure-based virtual screening (SBVS) to repurpose BTK inhibitors acalabrutinib, dasatinib, evobrutinib, fostamatinib, ibrutinib, inositol 1,3,4,5-tetrakisphosphate, spebrutinib, XL418 and zanubrutinib against SARS-CoV-2. Molecular docking is conducted with BTK inhibitors against structural and nonstructural proteins of SARS-CoV-2 and host targets (ACE2, TMPRSS2 and BTK). Molecular mechanics-generalized Born surface area (MM/GBSA) calculations and molecular dynamics (MD) simulations are then carried out on the selected complexes with high binding energy. Ibrutinib and zanubrutinib are found to be the most potent of the drugs screened based on the results of computational studies. Results further show that ibrutinib and zanubrutinib could exploit different mechanisms at the viral entry and replication stage and could be repurposed as potential inhibitors of SARS-CoV-2 pathogenesis.

Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches.

Background: Coronavirus (CoV) is an emerging human pathogen causing severe acute respiratory syndrome (SARS) around the world. Earlier identification of biomarkers for SARS can facilitate detection and reduce the mortality rate of the disease. Thus, by integrated network analysis and structural modeling approach, we aimed to explore the potential drug targets and the candidate drugs for coronavirus medicated SARS. Methods: Differentially expression (DE) analysis of CoV infected host genes (HGs) expression profiles was conducted by using the Limma. Highly integrated DE-CoV-HGs were selected to construct the protein-protein interaction (PPI) network.  Results: Using the Walktrap algorithm highly interconnected modules include module 1 (202 nodes); module 2 (126 nodes) and module 3 (121 nodes) modules were retrieved from the PPI network. MYC, HDAC9, NCOA3, CEBPB, VEGFA, BCL3, SMAD3, SMURF1, KLHL12, CBL, ERBB4, and CRKL were identified as potential drug targets (PDTs), which are highly expressed in the human respiratory system after CoV infection. Functional terms growth factor receptor binding, c-type lectin receptor signaling, interleukin-1 mediated signaling, TAP dependent antigen processing and presentation of peptide antigen via MHC class I, stimulatory T cell receptor signaling, and innate immune response signaling pathways, signal transduction and cytokine immune signaling pathways were enriched in the modules. Protein-protein docking results demonstrated the strong binding affinity (-314.57 kcal/mol) of the ERBB4-3cLpro complex which was selected as a drug target. In addition, molecular dynamics simulations indicated the structural stability and flexibility of the ERBB4-3cLpro complex. Further, Wortmannin was proposed as a candidate drug to ERBB4 to control SARS-CoV-2 pathogenesis through inhibit receptor tyrosine kinase-dependent macropinocytosis, MAPK signaling, and NF-kb singling pathways that regulate host cell entry, replication, and modulation of the host immune system. Conclusion: We conclude that CoV drug target "ERBB4" and candidate drug "Wortmannin" provide insights on the possible personalized therapeutics for emerging COVID-19.

Are the Allergic Reactions of COVID-19 Vaccines Caused by mRNA Constructs or Nanocarriers? Immunological Insights.

The Food and Drug Administration (FDA) has recently authorized the two messenger RNA (mRNA) vaccines BNT162b2 and mRNA-1273 for emergency use against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the COVID-19 coronavirus disease. BNT162b2 and mRNA-1273 vaccines were developed by Pfizer-BioNTech and Moderna, respectively, in 2020. The United Kingdom, Bahrain, Canada, Mexico, United States, Singapore, Oman, Saudi Arabia, Kuwait, and European Union began their vaccination programs with the BNT162b2 vaccine, while the United States and Canada also started the mRNA-1273 vaccination program in mid December 2020. On 28th December 2020, studies reported severe allergic reactions in people who received the BNT162b2, and few people who received the mRNA-1273 vaccine. Authors of the letter thus attempt to explore possible causes of anaphylaxis following COVID-19 vaccination.

Circulating miR-1246 Targeting UBE2C, TNNI3, TRAIP, UCHL1 Genes and Key Pathways as a Potential Biomarker for Lung Adenocarcinoma: Integrated Biological Network Analysis.

Analysis of circulating miRNAs (cmiRNAs) before surgical operation (BSO) and after the surgical operation (ASO) has been informative for lung adenocarcinoma (LUAD) diagnosis, progression, and outcomes of treatment. Thus, we performed a biological network analysis to identify the potential target genes (PTGs) of the overexpressed cmiRNA signatures from LUAD samples that had undergone surgical therapy. Differential expression (DE) analysis of microarray datasets, including cmiRNAs (GSE137140) and cmRNAs (GSE69732), was conducted using the Limma package. cmiR-1246 was predicted as a significantly upregulated cmiRNA of LUAD samples BSO and ASO. Then, 9802 miR-1246 target genes (TGs) were predicted using 12 TG prediction platforms (MiRWalk, miRDB, and TargetScan). Briefly, 425 highly expressed overlapping miRNA-1246 TGs were observed between the prediction platform and the cmiRNA dataset. ClueGO predicted cell projection morphogenesis, chemosensory behavior, and glycosaminoglycan binding, and the PI3K-Akt signaling pathways were enriched metabolic interactions regulating miRNA-1245 overlapping TGs in LUAD. Using 425 overlapping miR-1246 TGs, a protein-protein interaction network was constructed. Then, 12 PTGs of three different Walktrap modules were identified; among them, ubiquitin-conjugating enzyme E2C (UBE2C), troponin T1(TNNT1), T-cell receptor alpha locus interacting protein (TRAIP), and ubiquitin c-terminal hydrolase L1(UCHL1) were positively correlated with miR-1246, and the high expression of these genes was associated with better overall survival of LUAD. We conclude that PTGs of cmiRNA-1246 and key pathways, namely, ubiquitin-mediated proteolysis, glycosaminoglycan binding, the DNA metabolic process, and the PI3K-Akt-mTOR signaling pathway, the neurotrophin and cardiomyopathy signaling pathway, and the MAPK signaling pathway provide new insights on a noninvasive prognostic biomarker for LUAD.

Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations.

S-Sulfhydration of cysteine to the Cys-SSH persulfide is an oxidative post-translational modification that plays an important regulatory role in many physiological systems. Though hydrogen persulfide (H2S2) has recently been established as a signaling and cellular sulfhydration reagent, the chemistry and chemical biology of persulfides remain poorly explored. We first report an extensive high-level ab initio quantum chemical investigation of (H2S2)n, (H2S2)m·H2O, and (H2O)m·H2S2 clusters (n = 1-3 and m = 1, 2) and of H2S2 complexes with 19 compounds that model the side chains of naturally-occurring amino acids. The high polarizability of S necessitates the use of large, very diffuse, basis sets for proper description of H2S2 and its complexes. H2S2 possesses a skewed equilibrium geometry, with nonpolar trans and more polar cis conformers 6 and 8 kcal mol-1 higher in energy, respectively; the skewed conformation is preserved in all neutral and cationic complexes while a cis geometry prevails in some anionic complexes. H2S2 is found to be a better H-bond donor and a poorer acceptor than H2S, and that in complexes with H2O, alcohols and amines, H2S2 is a better H-bond donor. Radical delocalization on both S atoms stabilizes the perthiyl (HSS˙) over the thiyl (HS˙) radical and results in a ∼20 kcal mol-1 lower S-H homolytic bond dissociation in H2S2, making it a potential antioxidant. A simple additive model is optimized for H2S2 and used together with the TIP3P model and the CHARMM36 all-atom force field (FF) to investigate the structure and thermodynamic properties of liquid H2S2 and the solubility of H2S2 in water, and to model H2S2-protein interactions (for which new FF parameters are further developed). Very weak H-bonding characterizes liquid H2S2 and it is found immiscible in liquid water with a trend in H-bonding strengths between H2S2 and H2O in the order O-HO ≫ S-HO > O-HS. This work does not only provide a thorough description of the structure and energetics of H2S2 and its various complexes, but also yields a reliable FF for investigating H2S2 in chemistry and biology.

O4 -Alkylated-2-Deoxyuridine Repair by O6 -Alkylguanine DNA Alkyltransferase is Augmented by a C5-Fluorine Modification.

Oligonucleotides containing various adducts, including ethyl, benzyl, 4-hydroxybutyl and 7-hydroxyheptyl groups, at the O4 atom of 5-fluoro-O4 -alkyl-2'-deoxyuridine were prepared by solid-phase synthesis. UV thermal denaturation studies demonstrated that these modifications destabilised the duplex by approximately 10 °C, relative to the control containing 5-fluoro-2'-deoxyuridine. Circular dichroism spectroscopy revealed that these modified duplexes all adopted a B-form DNA structure. O6 -Alkylguanine DNA alkyltransferase (AGT) from humans (hAGT) was most efficient at repair of the 5-fluoro-O4 -benzyl-2'-deoxyuridine adduct, whereas the thymidine analogue was refractory to repair. The Escherichia coli AGT variant (OGT) was also efficient at removing O4 -ethyl and benzyl adducts of 5-fluoro-2-deoxyuridine. Computational assessment of N1-methyl analogues of the O4 -alkylated nucleobases revealed that the C5-fluorine modification had an influence on reducing the electron density of the O4 -Cα bond, relative to thymine (C5-methyl) and uracil (C5-hydrogen). These results reveal the positive influence of the C5-fluorine atom on the repair of larger O4 -alkyl adducts to expand knowledge of the range of substrates able to be repaired by AGT.

Benchmarking Rapid TLES Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study.

Standard molecular dynamics (MD) simulations of gas diffusion consume considerable computational time and resources even for small proteins. To combat this, temperature-controlled locally enhanced sampling (TLES) examines multiple diffusion trajectories per simulation by accommodating multiple noninteracting copies of a gas molecule that diffuse independently, while the protein and water molecules experience an average interaction from all copies. Furthermore, gas migration within a protein matrix can be accelerated without altering protein dynamics by increasing the effective temperature of the TLES copies. These features of TLES enable rapid simulations of gas diffusion within a protein matrix at significantly reduced (∼98%) computational cost. However, the results of TLES and standard MD simulations have not been systematically compared, which limits the adoption of the TLES approach. We address this drawback here by benchmarking TLES against standard MD in the simulation of O2 diffusion in myoglobin (Mb) as a case study since this model system has been extensively characterized. We find that 2 ns TLES and 108 ns standard simulations map the same network of diffusion tunnels in Mb and uncover the same docking sites, barriers, and escape portals. We further discuss the influence of simulation time as well as the number of independent simulations on the O2 population density within the diffusion tunnels and on the sampling of Mb's conformational space as revealed by principal component analysis. Overall, our comprehensive benchmarking reveals that TLES is an appropriate and robust tool for the rapid mapping of gas diffusion in proteins when the kinetic data provided by standard MD are not required. Furthermore, TLES provides explicit ligand diffusion pathways, unlike most rapid methods.

Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin's Gas Diffusion Tunnels.

Atomistic molecular dynamics simulations of diffusion of O2 from the hemes to the external solvent in the α- and ß-subunits of the human hemoglobin (HbA) tetramer reveal transient gas tunnels that are not seen in crystal structures. We find here that the tunnel topology, which encompasses the reported experimental Xe binding cavities, is identical in HbA's T, R, and R2 quaternary states. However, the O2 population in the cavities and the preferred O2 escape portals vary significantly with quaternary structure. For example, most O2 molecules escape from the T ß-subunit via the cavity at the center of the tetramer, but direct exit from the distal heme pocket dominates in the R2 ß-subunit. To understand what triggers the quaternary-linked redistribution of O2 within its tunnels, we examined how the simulated tertiary structure and dynamics of each subunit differs among T, R, and R2 and report that minor adjustments in α-chain dynamics and ß-heme position modulate O2 distribution and escape in HbA. Coupled to the ß-heme position, residue ßF71 undergoes quaternary-linked conformations that strongly regulate O2 migration between the ß-subunit and HbA's central cavity. Remarkably, the distal histidine (HisE7) remains in a closed conformation near the α- and ß-hemes in all states, but this does not prevent an average of 23, 31, and 46% of O2 escapes from the distal heme pockets of T, R, and R2, respectively, via several distal portals, with the balance of escapes occurring via the interior tunnels. Furthermore, preventing or restricting the access of O2 to selected cavities by mutating HisE7 and other heme pocket residues to tryptophan reveals how O2 migration adjusts to the bulky indole ring and sheds light on the experimental ligand binding kinetics of these variants. Overall, our simulations underscore the high gas porosity of HbA in its T, R, and R2 quaternary states and provide new mechanistic insights into why undergoing transitions among these states likely ensures effective O2 delivery by this tetrameric protein.

O2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7.

Hemoglobin transports O2 by binding the gas at its four hemes. Hydrogen bonding between the distal histidine (HisE7) and heme-bound O2 significantly increases the affinity of human hemoglobin (HbA) for this ligand. HisE7 is also proposed to regulate the release of O2 to the solvent via a transient E7 channel. To reveal the O2 escape routes controlled by HisE7 and to evaluate its role in gating heme access, we compare simulations of O2 diffusion from the distal heme pockets of the T and R states of HbA performed with HisE7 in its open (protonated) and closed (neutral) conformations. Irrespective of HisE7's conformation, we observe the same four or five escape routes leading directly from the α- or ß-distal heme pockets to the solvent. Only 21-53% of O2 escapes occur via these routes, with the remainder escaping through routes that encompass multiple internal cavities in HbA. The conformation of the distal HisE7 controls the escape of O2 from the heme by altering the distal pocket architecture in a pH-dependent manner, not by gating the E7 channel. Removal of the HisE7 side chain in the GlyE7 variant exposes the distal pockets to the solvent, and the percentage of O2 escapes to the solvent directly from the α- or ß-distal pockets of the mutant increases to 70-88%. In contrast to O2, the dominant water route from the bulk solvent is gated by HisE7 because protonation and opening of this residue dramatically increase the rate of influx of water into the empty distal heme pockets. The occupancy of the distal heme site by a water molecule, which functions as an additional nonprotein barrier to binding of the ligand to the heme, is also controlled by HisE7. Overall, analysis of gas and water diffusion routes in the subunits of HbA and its GlyE7 variant sheds light on the contribution of distal HisE7 in controlling polar and nonpolar ligand movement between the solvent and the hemes.

Effects of Cholesterol on the Thermodynamics and Kinetics of Passive Transport of Water through Lipid Membranes.

While it has long been known that cholesterol reduces the permeability of biological membranes to water, the exact mechanism by which cholesterol influences transmembrane permeation is still unclear. The thermodynamic and kinetic contributions to the transport of water across mixed DPPC/cholesterol bilayers of different composition are thus examined by molecular dynamics simulations. Our analyses show that cholesterol decreases transmembrane permeability to water mainly by altering the thermodynamics of water transport. In particular, the free-energy barrier to permeation is magnified in the dense bilayer interior and the partitioning of water is significantly lowered. The changes are observed to correlate quantitatively well with the cholesterol-dependent density and thickness of the bilayers. In contrast, diffusion coefficients are relatively insensitive to cholesterol concentration, except in the sparsely populated center of the bilayer. Diffusion of water in cholesterol-containing bilayers appears to be related to changes in the free area in the middle of the bilayer and to the solute cross-sectional area in the denser hydrophobic regions. Overall, cholesterol is found to have an inhibitory effect on the permeation of water at all concentrations investigated, although bilayers containing cholesterol concentrations up to 20 mol % display a more dramatic dependence on cholesterol content than at higher concentrations. Our results show that it is possible to quantitatively reproduce the relative effects of cholesterol on lipid bilayer permeability from molecular dynamics simulations.

Encapsulation of diatomic molecules in fullerene C60: implications for their main properties.

The endohedral complexes of diatomic guest molecules H2, N2, O2, F2, HF, CO, LiH, LiF, BN, and BeO with C60 have been characterized computationally by employing second-order Møller-Plesset (MP2) theory and its density-fitting local (DF-LMP2) variant. The interaction energies, equilibrium geometries, dipole moments and harmonic vibrational frequencies of these complexes have been systematically calculated. It was found that all guest molecules are stabilized inside the C60 cage, with the most pronounced stabilization effect (of about 50 kcal mol(-1)) observed for the polar covalent BeO and BN molecules. It is noteworthy that the normally short-lived BN molecule is the only guest molecule that was found to chemisorb on the inner surface of C60. When encapsulated, all guest molecules (except for BN) exhibit bond elongation (up to 0.07 Å) and, consequently, a red shift in vibrational stretching frequencies. In fact, the calculated vibrational properties of the H2@C60 complex agree well with those derived from experiment. The C60 geometry is not perturbed significantly upon encapsulation, but a subtle tendency to decrease the carbon-carbon bond alternation is observed. Polar guest molecules inside C60 are located at an off-center position and a significant decrease in their dipole moments upon encapsulation is observed. The importance of explicitly taking into account electron correlation effects, as well as full geometry relaxation, to yield a correct description of the complexes investigated is clearly demonstrated. The present results may serve as a guide for future attempts to synthesize such complexes employing the "molecular surgery" approach.

Density functional theory versus complete active space self-consistent field investigation of the half-metallic character of graphite-like and amorphous carbon nanoparticles.

Model carbon nanoparticles representative of the graphite-like and amorphous domains of active carbon are investigated with density functional theory (DFT) and complete active space self-consistent field (CASSCF) methods. Cyclic carbon clusters containing conjugated carbene groups are found to undergo Jahn-Teller distortion. More importantly, the half-metallicity, that is, the equal or similar stability of various spin states, previously suggested by DFT calculations for both types of nanosized clusters is confirmed by CASSCF calculations. Furthermore, the model carbon clusters are found to possess a multiconfigurational electronic structure dominated by high-spin configurations. When compared to CASSCF results, the single-reference DFT predicts proper electronic structures, characterized by antiferromagnetically coupled electron pairs, at the expense of spin contamination as a reflection of the multiconfigurational character. In fact, spin contamination, which is normally viewed as an error, does not corrupt the energetics of the half-metallic systems and therefore does not preclude the applicability of DFT to such systems.

Performance of density-functional tight-binding models in describing hydrogen-bonded anionic-water clusters.

Density-functional tight-binding (DFTB) models are computationally efficient approximations to density-functional theory that have been shown to predict reliable structural and energetic properties for various systems. In this work, the reliability and accuracy of the self-consistent-charge DFTB model and its recent extension(s) in predicting the structures, binding energies, charge distributions, and vibrational frequencies of small water clusters containing polyatomic anions of the Hofmeister series (carbonate, sulfate, hydrogen phosphate, acetate, nitrate, perchlorate, and thiocyanate) have been carefully and systematically evaluated on the basis of high-level ab initio quantum-chemistry [MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVQZ] reference data. Comparison with available experimental data has also been made for further validation. The self-consistent-charge DFTB model, and even more so its recent extensions, are shown to properly account for the structural properties, energetics, intermolecular polarization, and spectral signature of hydrogen-bonding in anionic water clusters at a fraction of the computational cost of ab initio quantum-chemistry methods. This makes DFTB models candidates of choice for investigating much larger systems such as seeded water droplets, their structural properties, formation thermodynamics, and infrared spectra.

Relaxation pathways of photoexcited iodide-methanol clusters: a computational investigation.

Upon photoexcitation of iodide-methanol clusters, I(-)(CH3OH)n, to a charge-transfer-to-solvent (CTTS) excited state, extensive relaxation was found to occur, accompanied by a convoluted modulation of the stability of the excited electron, which ultimately decreases substantially. In order to develop a molecular-level understanding of the relaxation processes of CTTS excited I(-)(CH3OH)n, high-level quantum chemical calculations are first used to investigate the ground, excited, and ionized states of I(-)(CH3OH)n (n = 2). Because of the relatively small size of I(-)(CH3OH)2, it was possible to characterize the contributions of solvent-solvent interactions to the stability of the CTTS excited cluster relative to dissociation into methanol, iodine, and a free electron, which exhibits a substantial dependence on the cluster geometric configuration. Ab initio molecular dynamics simulations of CTTS excited I(-)(CH3OH)3 are then performed to shed some light onto the nature of the relaxation pathways involved in the modulation of the stability of the excited electron in larger clusters. Simulation results suggest that separation of I and (CH3OH)3(-) accompanied by solvent reorganization in the latter can initially stabilize the excited electron, while gradual cluster fragmentation to I, (CH3OH)2(-), and CH3OH ultimately destabilizes it. This work shows, for the first time, that the inability of small CTTS excited I(-)(CH3OH)n to retain a solvated electron may be attributed to the limited hydrogen-bonding capacity of CH3OH, which increases the propensity for fragmentation to smaller clusters with lower excess-electron binding energies, and highlights the critical role of intricate molecular interactions in the electron solvation process.

Photoexcitation and charge-transfer-to-solvent relaxation dynamics of the I(-)(CH3CN) complex.

Photoexcitation of iodide-acetonitrile clusters, I(-)(CH3CN)n, to the charge-transfer-to-solvent (CTTS) state and subsequent cluster relaxation could result in the possible formation of cluster analogues of the bulk solvated electron. In this work, the relaxation process of the CTTS excited iodide-acetonitrile binary complex, [I(-)(CH3CN)]*, is investigated using rigorous ab initio quantum chemistry calculations and direct-dynamics simulations to gain insight into the role and motion of iodine and acetonitrile in the relaxation of CTTS excited I(-)(CH3CN)n. Computed potential energy curves and profiles of the excited electron vertical detachment energy for [I(-)(CH3CN)]* along the iodine-acetonitrile distance coordinate reveal for the first time significant dispersion effects between iodine and the excited electron, which can have a significant stabilizing effect on the latter. Results of direct-dynamics simulations demonstrate that [I(-)(CH3CN)]* undergoes dissociation to iodine and acetonitrile fragments, resulting in decreased stability of the excited electron. The present work provides strong evidence of solvent translational motion and iodine ejection as key aspects of the early time relaxation of CTTS excited I(-)(CH3CN)n that can also have a substantial impact on the subsequent electron solvation processes and further demonstrates that intricate details of the relaxation process of CTTS excited iodide-polar solvent molecule clusters make it heavily solvent-dependent.

Computational investigation of the hydration of alkyl diammonium chlorides and their effect on THF/water phase separation.

The solvation behavior of alkyl diammonium chlorides of varying alkyl chain length and the molecular details of their effect on the salting-out of organic molecules in aqueous phase have been investigated by classical molecular dynamics simulations. More specifically, systems containing water, tetrahydrofuran (THF), and their mixtures with α,ω-alkyl diammonium chlorides [H3N(CH2)nNH3]Cl2 (n = 2, 4, 6, 8, and 10) were simulated at ambient temperature and pressure. Various force fields were tested and one was chosen based on its ability to reproduce the physical properties of the pure THF solution and its mixture with water. Structural and thermodynamic analyses of the simulated salt-solvent mixtures reveal different extents of hydration of the dications depending on the alkyl chain length and indicate that the hydrophobic interactions between the dication alkyl chain and organic molecules play a key role in the solvation of the latter species. In fact, shorter dications are shown to promote THF/water phase separation, in agreement with previous experimental findings.