Theoretical study on the initial reaction mechanisms of <Emphasis Type="Italic">ansa</Emphasis>-metallocene zirconium precursor on hydroxylated Si(1 0 0) surface

The initial reaction mechanisms for depositing ZrO₂ thin films using ansa-metallocene zirconium (Cp₂CMe₂)ZrMe₂ precursor were studied by density functional theory (DFT) calculations. The (Cp₂CMe₂)ZrMe₂ precursor could be absorbed on the hydroxylated Si(1 0 0) surface via physisorption. Possible reaction pathways of (Cp₂CMe₂)ZrMe₂ were proposed. For each reaction, the activation energies and reaction energies were compared, and stationary points along the reaction pathways were shown. In addition, the influence of dispersion effects on the reactions was evaluated by non-local dispersion corrected DFT calculations.     

Locating structures and evolution pathways of reconstructed rutile TiO<Subscript>2</Subscript>(011) using genetic algorithm aided density functional theory calculations

Titanium dioxide (TiO₂) is an important metal oxide that has been used in many different applications. TiO₂ has also been widely employed as a model system to study basic processes and reactions in surface chemistry and heterogeneous catalysis. In this work, we investigated the (011) surface of rutile TiO₂ by focusing on its reconstruction. Density functional theory calculations aided by a genetic algorithm based optimization scheme were performed to extensively sample the potential energy surfaces of reconstructed rutile TiO₂ structures that obey (2?×?1) periodicity. A lot of stable surface configurations were located, including the global-minimum configuration that was proposed previously. The wide variety of surface structures determined through the calculations performed in this work provide insight into the relationship between the atomic configuration of a surface and its stability. More importantly, several analytical schemes were proposed and tested to gauge the differences and similarities among various surface structures, aiding the construction of the complete pathway for the reconstruction process.     

Theoretical insight into the sensitive mechanism of multilayer-shaped cocrystal explosives: compression and slide

Multilayer-shaped compression and slide models were employed to investigate the complex sensitive mechanisms of cocrystal explosives in response to external mechanical stimuli. Here, density functional theory (DFT) calculations implementing the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) with the Tkatchenko-Scheffler (TS) dispersion correction were applied to a series of cocrystal explosives: diacetone diperoxide (DADP)/1,3,5-trichloro-2,4,6-trinitrobenzene (TCTNB), DADP/1,3,5-tribromo-2,4,6-trinitrobenzene (TBTNB) and DADP/1,3,5-triiodo-2,4,6-trinitrobenzene (TITNB). The results show that the GGA-PBE-TS method is suitable for calculating these cocrystal systems. Compression and slide models illustrate well the sensitive mechanism of layer-shaped cocrystals of DADP/TCTNB and DADP/TITNB, in accordance with the results from electrostatic potentials and free space per molecule in cocrystal lattice analyses. DADP/TCTNB and DADP/TBTNB prefer sliding along a diagonal direction on the a?c face and generating strong intermolecular repulsions, compared to DADP/TITNB, which slides parallel to the b?c face. The impact sensitivity of DADP/TBTNB is predicted to be the same as that of DADP/TCTNB, and the impact sensitivity of DADP/TBTNB may be slightly more insensitive than that of DADP and much more sensitive than that of TBTNB.

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Graphical Abstract Theoretical insights into the sensitive mechanism of multilayer-shaped cocrystal explosives: compression and slide

     

Theoretical study of the interaction between molecular oxygen and tetraaza macrocyclic manganese complexes

Theoretical chemistry calculations using the Density Functional Theory (DFT) were carried out to understand the interaction between oxygen (O₂) and MnN₄ type manganese-based complexes during the formation of MnN₄-O₂ adducts. In order to understand how this interaction is affected by different macrocyclic ligands, O₂ was bonded to manganese-porphyrin (MnP), manganese-octamethylporphyrin (MnOMP), manganese-tetraaza[14]annulene (MnTAA), manganese-dibenzo [b,i] [1, 4, 8, 11]-tetraaza [14] annulene (MnDBTAA), manganese-2,3,9,10-tetramethyl-1,4,8,11-tetraazacyclotetradeca-1,3,8,10-tetraene ([(tim)Mn]²⁺), and manganese-2,3,9,10-tetraphenyl-1,4,8,11-tetraazacyclotetradeca-1,3,8,10-tetraene ([(ph-tim)Mn]²⁺). The binding and activation of the oxygen molecule was facilitated by an increasing trend in the O-O bond lengths and a decreasing one in the O-O vibrational frequency, with preference for the O₂ side-on interaction among MnN₄ macrocycles. The catalytic activities of the MnN₄ complexes toward the O₂ binding process increased in the following order: [(ph-tim)Mn]²⁺?<?MnP?<?MnOMP?<?MnDBTAA?<?MnTAA?<?[(tim)Mn]²⁺. Therefore, it was concluded that the [(tim)Mn]²⁺complex was the most active for the binding and activation of molecular oxygen.     

Is photoisomerization required for NO photorelease in ruthenium nitrosyl complexes?

The factors that explain the competition between intramolecular NO linkage photoisomerization and NO photorelease in five ruthenium nitrosyl complexes were investigated. By applying DFT-based methods, it was possible to characterize the ground states and lowest triplet potential energy surfaces of these species, and to establish that both photoisomerization and photorelease processes can occur in the lowest triplet state of each species. This work highlights the crucial role of the sideways-bonded isomer, a metastable state also known as the MS2 isomer, in the photochemical loss of NO, while the results obtained also indicate that the population of the triplet state of this isomer is compulsory for both processes and show how photoisomerization and photorelease interfere.

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Graphical Abstract Illustration of the crucial role of the ³MS2 state in the photoreactivities of ruthenium nitrosyl complexes

     

Investigating the effects of point mutations on the affinity between the cyanobacterial lectin microvirin and high mannose-type glycans present on the HIV envelope glycoprotein

Human immunodeficiency virus (HIV) infections continue to exert an enormous impact on global human health. This led experts to emphasize the importance of new measures for preventing HIV infections, including the development of vaccines and novel drugs. In this context, a promising approach involves the use of lectins that can bind the surface envelope glycoprotein gp120 of HIV with high affinity, preventing viral entry. The cyanobacterial lectin microvirin (MVN) has been proposed as a candidate for development as a topical microbicide because of its ability to bind to high mannose-type glycans, potently inhibiting HIV-1 entry. Thus, the aim of this computational study was to investigate the effects of four point mutations (D53Q, D53E, D53K, and D53W) on the structure and affinity of MVN with di-mannose (MAN). Molecular dynamics simulations followed by binding free energy calculations using MM-GBSA were employed. The calculated binding free energy of ligand-receptor complexation of MVN with MAN was ?26.02 kcal mol^-1. We identified in the wild-type protein that residues I45, T59, and Q81 have a major contribution to the binding free energy of di-mannose. Among the investigated mutants, the most promising one was the D53W mutation, with a theoretical binding free energy value of ?29.16 kcal mol^-1. We suggest that this increased stability is due to the introduction of extra rigidity on the hinge region connecting two key structural elements of the MVN binding site.     

Theoretical insights into the stabilities,detonation performance,and electrostatic potentials of cocrystals containing α- or β-HMX and TATB,FOX-7, NTO,or DMF in various molar ratios

A molecular dynamics method was employed to study the binding energies associated with the cocrystallization (at selected crystal planes) of either 1,3,5-triamino-2,4,6-trinitro-benzene (TATB), 1,1-diamino-2,2-dinitroethylene, 3-nitro-1,2,4-triazol-5-one (TATB, FOX-7, and NTO, respectively, all of which are explosives), or N,N-dimethylformamide (DMF, a nonenergetic solvent) in various molar ratios with 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane in its α and β conformations (α-HMX and β-HMX, respectively). The results showed that the cocrystals with low molar ratios (2:1, 1:1, 1:2, and 1:3) were the most stable. The binding energies of HMX/NTO and HMX/DMF were larger than those of HMX/TATB and HMX/FOX-7. According to the calculated stabilities, HMX prefers to adopt its α form in HMX/TATB and its β form in HMX/NTO, whereas the two forms coexist in HMX/FOX-7. For HMX/TATB, HMX/NTO, and α-HMX/FOX-7, increasing the proportion of the cocrystal component with the highest detonation heat (HMX in the first two cases, FOX-7 in the latter) increases the detonation heat, velocity, and pressure of the cocrystal. However, increasing the proportion of the component with the highest detonation heat in β-HMX/FOX-7 and γ-CL-20/FOX-7 increases the detonation heat of the cocrystal but decreases its detonation velocity. An investigation of the surface electrostatic potential revealed how the sensitivity changes upon cocrystal formation.

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Graphical Abstract Surface electrostatic potential of HMX/TATB

     

Density functional study of H<Subscript>2</Subscript>O molecule adsorption on α-U(001) surface

Periodic density functional theory (DFT) calculations were performed to investigate the adsorption of H₂O on U(001) surface. The metallic nature of uranium atom and different adsorption sites of U(001) surface play key roles in the H₂O molecular dissociate reaction. The long-bridge site is the most favorable site of H₂O-U(001) adsorption configuration. The triangle-center site of the H atom is the most favorable site of HOH-U(001) adsorption configuration. The interaction between H₂O and U surface is more evident on the first layer than that on any other two sub-layers. The dissociation energy of one hydrogen atom from H₂O is ?1.994 to ?2.215 eV on U(001) surface, while the dissociating energy decreases to ?3.351 to ?3.394 eV with two hydrogen atoms dissociating from H₂O. These phenomena also indicate that the O_ads can promote the dehydrogenation of H₂O. A significant charge transfer from the first layer of the uranium surface to the H and O atoms is also found to occur, making the bonding partly ionic.     

Omentin protects against LPS-induced ARDS through suppressing pulmonary inflammation and promoting endothelial barrier via an Akt/eNOS-dependent mechanism

Acute respiratory distress syndrome (ARDS) is characterized by increased pulmonary inflammation and endothelial barrier permeability. Omentin has been shown to benefit obesity-related systemic vascular diseases; however, its effects on ARDS are unknown. In the present study, the level of circulating omentin in patients with ARDS was assessed to appraise its clinical significance in ARDS. Mice were subjected to systemic administration of adenoviral vector expressing omentin (Ad-omentin) and one-shot treatment of recombinant human omentin (rh-omentin) to examine omentin''s effects on lipopolysaccharide (LPS)-induced ARDS. Pulmonary endothelial cells (ECs) were treated with rh-omentin to further investigate its underlying mechanism. We found that a decreased level of circulating omentin negatively correlated with white blood cells and procalcitonin in patients with ARDS. Ad-omentin protected against LPS-induced ARDS by alleviating the pulmonary inflammatory response and endothelial barrier injury in mice, accompanied by Akt/eNOS pathway activation. Treatment of pulmonary ECs with rh-omentin attenuated inflammatory response and restored adherens junctions (AJs), and cytoskeleton organization promoted endothelial barrier after LPS insult. Moreover, the omentin-mediated enhancement of EC survival and differentiation was blocked by the Akt/eNOS pathway inactivation. Therapeutic rh-omentin treatment also effectively protected against LPS-induced ARDS via the Akt/eNOS pathway. Collectively, these data indicated that omentin protects against LPS-induced ARDS by suppressing inflammation and promoting the pulmonary endothelial barrier, at least partially, through an Akt/eNOS-dependent mechanism. Therapeutic strategies aiming to restore omentin levels may be valuable for the prevention or treatment of ARDS.Acute respiratory distress syndrome (ARDS) is a devastating condition with a 30–60% mortality rate.^{1, 2} Although the pathogenesis of ARDS is complex, the inflammatory response and endothelial barrier disruption play important roles in the development of ARDS.^{3, 4, 5} Therefore, in addition to conventional anti-inflammatory treatments, therapeutic strategies aim to restore pulmonary endothelial barrier integrity and function through regulating inter-endothelial AJs and the endothelial cytoskeleton to minimize protein leakage and leukocyte infiltration under ARDS conditions.^{6, 7}Obesity, especially visceral obesity, has clearly been shown to impair systemic vasculature and to lead to the initiation and progression of vascular disorders.^{8, 9, 10} Although different from the well-documented impacts of obesity on cardiovascular disease, the relationships between obesity and ARDS have not been well elucidated. Clinical and experimental data focused on pertinent physiological changes in obesity indicate that the obesity may alter ARDS pathogenesis by ‘priming'' the pulmonary endothelial barrier for insult and amplifying the early inflammatory response, thus lowering the threshold to initiate ARDS.^{11, 12} Contrary to conventional dogma, adipose tissue is now appreciated as an important endocrine tissue that secretes various bioactive molecules called adipokines, which contribute to the progression of diverse vascular diseases, including hypertension, cardiovascular disease and atherosclerosis.^{13, 14, 15, 16} Although ARDS is not a classified pulmonary vascular disease, it is a severe inflammatory lung condition with widespread pulmonary endothelial breakdown. Clinical evidence has indicated that the obesity might be an emerging risk factor for ARDS and that circulating adipokines levels are associated with the initiation and progression of ARDS.^{11, 12, 17, 18} Moreover, experimental studies have suggested that some anti-inflammatory adipokines, such as adiponectin and apelin, exert beneficial actions on ARDS.^{19, 20, 21}Omentin is an anti-inflammatory adipokine that is abundant in human visceral fat tissue.^{22, 23} Paradoxically, higher circulating omentin-1 levels are present in lean and healthy individuals compared with the obese and diabetic patients. Moreover, as a novel biomarker of endothelial dysfunction, reduced circulating omentin levels are related to the pathological mechanism of obesity-linked vascular disorders, including type 2 diabetes, atherosclerosis, hypertension and cardiovascular disease.^{24, 25, 26, 27, 28} Furthermore, experimental studies have found that omentin stimulates vasodilation in isolated blood vessels and suppresses cytokine-stimulated inflammation in endothelial cells (ECs).^{29, 30, 31} Thus, these data suggest that omentin may protect against obesity-related vascular complications through its anti-inflammatory and vascular-protective properties; however, little is known regarding its role in lung tissue. It was reported that decreased circulating omentin-1 levels could be regarded as an independent predictive marker for the obstructive sleep apnea syndrome and that omentin protects against pulmonary arterial hypertension through inhibiting vascular structure remodeling and abnormal contractile reactivity.^{32, 33, 34} However, to our knowledge, no study has assessed the impact of omentin on ARDS.Akt-related signaling pathways function as an endogenous negative feedback mechanism in response to the injurious stimulus. Our prior studies have demonstrated that Akt-related signaling contributes to protection against ARDS.^{35, 36} Moreover, omentin has been reported to exert anti-inflammatory, pro-survival and pro-angiogenic functions in various cells via an Akt-dependent mechanism.^{30, 31, 37, 38, 39, 40, 41, 42}Collectively, given that ARDS is ultimately an obesity-related disorder of vascular function and that omentin is a favorable pleiotropic adipokine capable of anti-inflammatory, pro-angiogenic and anti-apoptotic abilities; omentin may exert beneficial effects on ARDS. In the present study, we first aimed to appraise the clinical significance of omentin in ARDS and then specifically evaluated its impact on inflammation and the endothelial barrier. Furthermore, we mechanistically investigated the role of Akt-related signaling pathways in these effects induced by omentin in vivo and in vitro.