Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

Generation of 3-aminopropanamide and its cluster formation with nucleation precursors- a theoretical exploration

Aminoamides are formed in the atmospheric environments by the auto-oxidation of the parent diamines. In this work, the oxidation chemistry of diamine (1,3-Diaminopropane, Dap) to the amino amide (3- aminopropanamide, 3-APA) and its new particle formation potential with small atmospheric molecules such as NH3 (A), H2O (W) and H2SO4 (SA) are theoretically investigated using the M062X/6-311++G** theory. The bimolecular rate coefficient of the ·OH initiated H-atom abstraction is computed to be 1.01 × 10-11 cm3 molecule-1 s-1. Further reaction of the peroxy radical intermediate indicates that the pathway involving γ H- shift of the initially formed radical intermediates to be more favourable on kinetic grounds with the effective bimolecular rate coefficient of 3.87 × 10-14 cm3 molecule-1s-1. The thermodynamic barrier associated with the H-shifts involved in this pathway is in the range of 13-20 kcal/mol. The cluster formation of APA with SA is more favourable than the clusters with W and A, wherein the free energy of formation of (APA)(SA) and (APA)(SA)2 are -11.3 and -22.6 kcal/mol, respectively. However, the feasibility of cluster formation with W and A increases with the altitude and becomes spontaneous in the case of water at an altitude of 12 km. The present work indicates that aminoamides like 3-APA can participate in the initial stages of new particle formation events by forming clusters with SA molecules. The scattering parameters and topological analysis of different (Amide)(SA) clusters indicate more scattering properties for the (APA)(SA) cluster, which has an adverse effect on the atmosphere. Furthermore, topological analysis indicates that H-bond formation is more prominent in the (APA)(SA) cluster.

Nitrogen Removal from Landfill Leachate Using Biochar Derived from Wheat Straw

Landfill leachate (LLCH) disposal poses challenges due to high pollutant concentrations. This study investigates the use of biochar (BC) derived from wheat straw for nitrogen content reduction. Laboratory experiments evaluated BC's adsorption capacity (qm) for nitrogen removal from ammonium chloride solution (NH4Cl) and LLCH, along with testing isotherm models. The results demonstrated that BC was more efficient (95.08%) than commercial activated carbon AC (93.11%), the blank, in adsorbing nitrogen from NH4Cl. This superior performance of BC may be attributed to its higher carbon content (57.74%) observed through elemental analysis. Lower results for BC/LLCH may be due to LLCH's complex chemical matrix. The Langmuir isotherm model best described BC/NH4Cl adsorption (qm = 0.5738 mg/g). The AC/NH4Cl data also fitted into the Langmuir (R2 ˃ 0.9) with a qm of 0.9469 mg/g, and 26.667 mg/g (R2 ˂ 0.9) was obtained for BC/LLCH; the BC/LLCH also gave higher qm (R2 ˃ 0.9) using the Jovanovich model (which also follows Langmuir's assumptions). The mean energy of the adsorption values estimated for the AC/NH4Cl, BC/NH4Cl, and BC/LLCH processes were 353.55, 353.55, and 223.61 kJ/mol, respectively, suggesting that they are all chemisorption processes and ion exchange influenced their adsorption processes. The Freundlich constant (1/n) value suggests average adsorption for BC/LLCH. The BC/LLCH data followed the Harkins-Jura model (R2: 0.9992), suggesting multilayered adsorption (or mesopore filling). In conclusion, biochar derived from wheat straw shows promising potential for landfill leachate remediation, offering efficient nitrogen removal capabilities and demonstrating compatibility with various adsorption models. This research also lays the groundwork for further exploration of other biochar-based materials in addressing environmental challenges associated with landfill leachate contamination.

Supersonic jet chirped pulse microwave spectroscopy of ring-like methanol : water pentamers

The potential energy surfaces of pure methanol and mixed methanol-water pentamers have been explored using chirped pulse Fourier-transform microwave spectroscopy aided by ab initio calculations. Rotational constants, anharmonic corrections, dipole moments, and relative energies were calculated for different conformers. Predicted rotational transitions were then fit to experimental spectra from 10-18 GHz and the assignments were confirmed using double resonance experiments where feasible. The results show all 23 of the lowest energy conformers are bound in a planar ring of hydrogen bonding that display a steady decrease in the RO-O distance along this ring as methanol content is increased. Interspersed methanol and water conformers have comparable relative abundances to those with micro-aggregation, but structures with micro-aggregated methanol and water have a higher rigid rotor fitting error. The computational methods' high degree of accuracy when compared to our experimental results suggests the strong donor-acceptor hydrogen bonding in these clusters leads to well-defined minima on the intermolecular potential energy surface.

Development of Green HPTLC method for simultaneous determination of a promising combination Tamsulosin and Mirabegron: stability-indicating assay was examined

Recently, mirabegron has been added to tamsulosin to treat overactive bladder in men with benign prostatic hypertrophy. A Rapid, selective, sensitive, and green high-performance thin-layer chromatography (HPTLC) approach was developed for the simultaneous determination of tamsulosin (TAM) and mirabegron (MIR) in pure and laboratory-prepared mixture. Complete separation was obtained on silica gel F254 using the solvent system methanol-ethyl acetate-ammonia (3:7:0.1, v/v). Short-wave ultraviolet light at 270 nm was used to view the chromatographic bands. For MIR and TAM, the suggested technique revealed compact spots with retention factor Rf values of 0.42 and 0.63, respectively. Within concentration ranges of 0.15-7.5 µg/band and 0.05-2.5 µg/band, good linearity was observed, with mean percentage recoveries of 100.04 ± 0.56 and 99.98% ± 0.95 for MIR and TAM, respectively. Green assessment of the developed HPTLC technique was estimated using different green analytical chemistry metrics such as Analytical eco-scale Analytical GREEness (AGREE), and Green Analytical Procedure Index (GAPI) metrics. The proposed method was effectively used as a stability-indicating assay to assess the presence of MIR and TAM in the pharmaceutical dosage form in the presence of their degradation product. The statistical analysis showed high precision and accuracy.

Computational chemistry of cluster: Understanding the mechanism of atmospheric new particle formation at the molecular level

New particle formation (NPF), which exerts significant influence over human health and global climate, has been a hot topic and rapidly expands field of research in the environmental and atmospheric chemistry recent years. Generally, NPF contains two processes: formation of critical nucleus and further growth of the nucleus. However, due to the complexity of the atmospheric nucleation, which is a multicomponent process, formation of critical clusters as well as their growth is still connected to large uncertainties. Detection limits of instruments in measuring specific gaseous aerosol precursors and chemical compositions at the molecular level call for computational studies. Computational chemistry could effectively compensate the deficiency of laboratory experiments as well as observations and predict the nucleation mechanisms. We review the present theoretical literatures that discuss nucleation mechanism of atmospheric clusters. Focus of this review is on different nucleation systems involving sulfur-containing species, nitrogen-containing species and iodine-containing species. We hope this review will provide a deep insight for the molecular interaction of nucleation precursors and reveal nucleation mechanism at the molecular level.

Tanshinone IIA reduces AQP4 expression and astrocyte swelling after OGD/R by inhibiting the HMGB1/RAGE/NF-κB/IL-6 pro-inflammatory axis

This study aimed to investigate the role of tanshinone IIA (TSO IIA) in astrocytic swelling caused by ischemia–reperfusion-like injury in an in vitro model and the molecular mechanisms underlying this effect. Primary brain astrocytes were cultured under conditions of glucose and oxygen deprivation and reoxygenation (OGD/R). The study explored the effects of TSO IIA treatment on cell swelling and injury and the protein levels of aquaporin 4 (AQP4) in the plasma membrane. It then examined the involvement of the high-mobility group box protein 1 (HMGB1)/receptors for advanced-glycation end products (RAGE)/nuclear factor-kappa B (NF-κB)/interleukin-6 (IL-6) pro-inflammatory axis in TSO IIA-mediated protection. The treatment with TSO IIA alleviated OGD/R-induced astrocytic swelling and the overclustering of AQP4 protein in the plasma membrane. In addition, TSO IIA significantly reduced the overexpression of HMGB1 and the high levels of the NF-κB protein in the nucleus and of the IL-6 protein in the cytoplasm and extracellular media induced by OGD/R. The combination of TSO IIA and recombinant HMGB1 reversed these effects. The inhibition of the RAGE, the receptor of HMGB1, induced results similar to those of TSO IIA. In addition, exogenous IL-6 reversed TSO IIA-mediated effect on AQP4 overclustering and cell swelling. TSO IIA significantly reduced astrocyte swelling after OGD/R injury in vitro, via blocking the activation of the HMGB1/RAGE/NF-κB/IL-6 pro-inflammatory axis and thereby decreasing the expression of AQP4 in the plasma membrane.

Amide-Driven Secondary Building Unit Structural Transformations between Zn(II) Coordination Polymers

The behavior of coordination polymers (CPs) against external stimuli has witnessed remarkable attention, especially when the resulting CPs present reversible molecular arrays. Accordingly, CPs with these characteristics can lead to differences in their properties owing to these structural differences, being promising for their use as potential molecular switches with diverse applications. Herein, we have synthesized four Zn(II) CPs bearing α-acetamidocinnamic acid (HACA) and 4,4'-bipyridine (4,4'-bipy). The reaction between Zn(OAc)₂·2H₂O, HACA, and 4,4'-bipy yields {[Zn(ACA)₂(4,4'-bipy)]·EtOH} _n (1), which was used for the formation of three CPs through dissolution-recrystallization structural transformations (DRSTs): {[Zn(ACA)₂(4,4'-bipy)]·2MeOH} _n (2), {[Zn₂(μ-ACA)₂(ACA)₂(4,4'-bipy)]·2H₂O} _n (3), and {[Zn₃(μ-ACA)₆(4,4'-bipy)]·0.75CHCl₃} _n (4). The study of the four crystal structures revealed that their secondary building units (SBUs) comprise monomeric, dimeric, and trimeric arrangements linked by 4,4'-bipy ligands. The fundamental role of the utilized solvent and/or temperature, as well as their effect on the orientation of the amide moieties driving the formation of the different SBUs is discussed. Furthermore, the reversibility and interconversion between the four CPs have been assayed. Finally, their solid-state photoluminescence has evinced that the effect of the amide moieties not only predetermine a different SBU but also lead to a different emission in 4 compared with 1-3.

Molecular Interactions between Amino Silane Adhesion Promoter and Acrylic Polymer Adhesive at Buried Silica Interfaces

In this study, the influence of an amino silane (3-(2-aminoethylamino)-propyldimethoxymethylsilane, AEAPS) on the interfacial structure and adhesion of butyl acrylate/methyl methacrylate copolymers (BAMMAs) to silica was investigated by sum frequency generation vibrational spectroscopy (SFG). Small amounts of methacrylic acid, MAA, were included in the BAMMA polymerizations to assess the impact of carboxylic acid functionality on the glass interface. SFG was used to probe the O-H and C═O groups of incorporated MAA, ester C═O groups of BAMMA, and CH groups from all species at the silica interfaces. The addition of AEAPS resulted in a significant change in the molecular structure of the polymer at the buried interface with silica due to specific interactions between the BAMMA polymers and silane. SFG results were consistent with the formation of ionic bonds between the primary and secondary amines of the AEAPS tail group and the MAA component of the polymer, as evidenced by the loss of the MAA O-H and C═O signals at the interface. It is extensively reported in the literature that methoxy head groups of an amino silane chemically bind to the silanols of glass, leaving the amine groups available to react with various chemical functionalities. Our results are consistent with this scenario and support an adhesion promotion mechanism of amino silane with various aspects: (1) the ionic bond formation between the tail amine group and acid functionality on BAMMA, (2) the chemical coupling between the silane head group and glass, (3) migration of more ester C═O groups to the interface with order, and (4) disordering or reduced levels of CH groups at the interface. These results are important for better understanding of the mechanisms and effect of amino silanes on the adhesion between acrylate polymers and glass substrates in a variety of applications.

Role of hydrogen bonding in bulk aqueous phase decomposition, complexation, and covalent hydration of pyruvic acid

The behavior of hydrogen bonding changes between the gas and aqueous phase, altering the mechanisms of various pyruvic acid processes and consequently affecting the aerosol formation in different environments.

The potential mechanism of atmospheric new particle formation involving amino acids with multiple functional groups

Amino acids are recognized as significant components of atmospheric aerosols. However, their potential role in atmospheric new particle formation (NPF) is poorly understood, especially aspartic acid (ASP), one of the most abundant amino acids in the atmosphere. It has not only two advantageous carboxylic acid groups but also one amino group, both of which are both effective groups enhancing NPF. Herein, the participation mechanism of ASP in the formation of new particle involving sulfuric acid (SA)-ammonia (A)-based system has been studied using the Density Functional Theory (DFT) combined with the Atmospheric Clusters Dynamic Code (ACDC). The results show that the addition of ASP molecules in the SA-A-based clusters provides a promotion on the interaction between SA and A molecules. Moreover, ACDC simulations indicate that ASP could present an obvious enhancement effect on SA-A-based cluster formation rates. Meanwhile, the enhancement strength R presents a positive dependence on [ASP] and a negative dependence on [SA] and [A]. Besides, the enhancement effect of ASP is compared with that of malonic acid (MOA) with two carboxylic acid groups (Chemosphere, 2018, 203, 26-33), and ASP presents a more obvious enhancement effect than MOA. The mechanism of NPF indicates that ASP could contribute to cluster formation as a "participator" which is different from the "catalytic" role of MOA at 238 K. These new insights are helpful to understand the mechanism of NPF involving organic compounds with multiple functional groups, especially the abundant amino acids, such as the ASP, in the urban/suburban areas with intensive human activities and industrial productions and therefore the abundant sources of amino acids. Furthermore, the NPF of the SA-A-based system involving amino acid should be considered when assessing the environmental risk of amino acid.

Exploring the Role of Asp1116 in Selective Drug Targeting of CREBcAMP- Responsive Element-binding Protein Implicated in Prostate Cancer

BACKGROUND

The selective targeting of CREB-cAMP-responsive element-binding protein (CBP) has recently evolved as a vital therapeutic approach for curtailing its aberrant upregulation associated with the development of prostate cancer. Inhibition of CBP has been discovered to be an important therapeutic option in androgen receptor signalling pathway mediated prostate cancer. Y08197, a novel selective inhibitor of CBP, has shown promising therapeutic outcome in prostate carcinogenesis over non-selective analogues such as CPI-637.

METHODS/RESULTS

Herein, we used molecular dynamics simulation to gain insights into the mechanistic and selective targeting of Y08197 at the bromodomain active site. Molecular Mechanics/ Poisson-Boltzmann Surface Area (MM/PBSA) analysis revealed a similar inhibitory effect between Y08197 and CPI-637. Furthermore, in exploring the selective affinity of Y08197 towards CBP in combination with Bromodomain and PHD finger-containing protein 1(BRPF1), our findings highlighted Asp1116 as the 'culprit' residue responsible for this selective targeting. Upon binding, Asp1116 assumed a conformation that altered the architecture of the bromodomain active site, thereby orienting the helices around the active site in a more compacted position. In addition to some specific structural perturbations mediated by Asp1116 on the dynamics of CBP, our study revealed that the strong hydrogen bond interaction (N-H...O) elicited in CBP-Y08197 sequestered Y08197 tightly into the CBP bromodomain active site.

CONCLUSION

Conclusively, the inhibition and selective pattern of Y08197 can be replicated in future structure-based CBP inhibitors and other bromodomain implicated in carcinogenesis.

Propionamide participating in H2SO4-based new particle formation: a theory study

Propionamide (PA), an important pollutant emitted into the atmosphere from a variety of sources, is abundant in many areas worldwide, and could be involved in new particle formation (NPF). In this study, the enhancement of the H₂SO₄ (SA)-based NPF by PA was evaluated through investigating the formation mechanism of (PA)_m(SA)_n (m = 0–3 and n = 0–3) clusters using computational chemistry and kinetics modeling. Our study proved that the formation of all the PA-containing clusters is thermodynamically favorable. Furthermore, the Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O group in PA plays an important role in the clusters with more PA than SA, and the basicity of bases exerts a greater influence with an increasing amount of SA. We demonstrate that although the enhancing potential of PA is lower than that of the strongest enhancers of SA-based NPF such as methylamine (MA) and dimethylamine (DMA), PA can enhance the SA-based NPF at the parts per billion (ppb) level, which is typical for concentrations of C₃-amides in, for example, urban Shanghai (China). The monomer evaporation is the dominant degradation pathway for the (PA)_m(SA)_n clusters, which differs from that of the SA–DMA system. The formation rate of PA-containing clusters is comparable to the rate coefficients for PA oxidation by hydroxyl (OH) radicals, indicating that participating in the SA-based NPF is a crucial sink for PA.

Propionamide (PA), an important pollutant emitted into the atmosphere from a variety of sources, is abundant in many areas worldwide, and could be involved in new particle formation (NPF).

A density functional theory study of the molecular interactions between a series of amides and sulfuric acid

Amides, a class of nitrogen-containing organic pollutants in the atmosphere, may affect the formation of atmospheric aerosols by the interactions with sulfuric acid. Here, the molecular interactions of sulfuric acid with formamide, methylformamide, dimethylformamide, acetamide, methylacetamide and dimethylacetamide was investigated by density functional theory. Geometry optimization and Gibbs free energy calculation were carried out at M06-2X/6-311++G(3df,3pd) level. The results indicate that the addition of amides to H₂SO₄ might have a promoting effect on atmospheric new particle formation at 298.15 K and 1 atm. In the initial stage of new particle formation, the binding capacity of amides and sulfuric acid is stronger than ammonia, but weaker than methylamine. It is worth noting that the trans-methylacetamide could have similar capabilities of stabilizing sulfuric acid as dimethylamine. In the presence of water, amides are found to only have a weak enhancement capability on new particle formation. In addition, we can infer from evaporation rate that the small molecule clusters of formamide and sulfuric acid may be more energetically favorable than macromolecule clusters.

Gas phase transformation from organic acid to organic sulfuric anhydride: Possibility and atmospheric fate in the initial new particle formation

New particle formation (NPF) process has been observed frequently in various environments and produces a large fraction of atmospheric aerosols. However, the chemical species participating in the nucleation as well as the corresponding nucleation mechanism in the atmosphere still remain ambiguous. Recent research by Leopold et al. shows that cycloaddition reaction of SO₃ to carboxylic acids could contribute to the formation of organic sulfuric anhydride which would have lower vapor pressure compared with the corresponding carboxylic acid and hence kick-start new particle formation in the gas phase. In the present study, energy profile for the formation of 3-methyl-1,2,3-butanetricarboxylic sulfuric anhydride (MBTCSA) through the cycloaddition of SO₃ to 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA) has been investigated using computational methods. As a result, such a process would be effectively barrierless for one of the terminal carboxy group and has very low energy barriers for the other two carboxy groups (0.6 and 2.8 kcal/mol, respectively), indicating the whole process is a plausible gas phase pathway to MBTCSA formation. Furthermore, by evaluating the stability of the generated atmospheric clusters through topological and kinetic analysis, interaction between atmospheric nucleation precursor with MBTCSA is found to be more thermodynamically favourable and stronger than those with sulfuric acid and MBTCA which is identified from further-generation oxidation of a-pinene. Hence MBTCSA is speculated to be a potential participator in the initial new particle formation and the further particles growth.

The potential role of malonic acid in the atmospheric sulfuric acid - Ammonia clusters formation

Malonic acid (MOA), one of the major dicarboxylic acids (DCAs) in aerosols, has been identified experimentally and computationally to be a strong acid. However, its potential role in the atmospheric clusters formation is still ambiguous. Hence, the participant mechanism of MOA on the formation of atmospheric sulfuric acid (SA)- ammonia (A) clusters was investigated by combining computational methods with atmospheric cluster dynamics code (ACDC). The most stable molecular structures obtained at the M06-2X/6-311++G(3df,3pd) level of theory shows that the added MOA molecule in the SA-A-based clusters presents a promotion on the interactions between SA and A molecules. ACDC simulations indicate directly an obvious enhancement strength R_MOA on the clusters formation rates at 218 K and the concentration of MOA ([MOA]) larger than 10⁸ molecules cm^-3, up to five orders of magnitude. Meanwhile, enhancement strength of MOA is compared with that of glycolic acid, and as expected, MOA presents a superior enhancement strength. Both R_MOA and the compared enhancement strength (r_com) present a positive dependency on [MOA] and a negative dependency on [SA]. With the increase of [A], both R_MOA and r_com (except at [SA] = 10⁴ molecules cm^-3) first increase, reaching the maximum value and then decrease. Finally, a catalytic participant mechanism of MOA where MOA acts as a mediate bridge for the formation of pure SA-A-based clusters has been identified by tracing the main growth pathways of the system.

Unravelling hydrogen bonding interactions of tryptamine–water dimer from neutral to cation

The physical origin for the three intermolecular hydrogen bonds in the neutral and cationic forms of the tryptamine–water dimer is explored.