Molecular dynamics simulation of the effect of temperature on the conformation of ubiquitin protein.

CONTENT: Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond. METHODS: All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8 nm, a setting that allowed > 0.8 nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100 kJ/mol·nm with a 0.01 nm step size. Minimization was followed by 30 ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10 ns without any restraint using an integral time step of 1 fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5 nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2 nm.

Density Functional Theory Study of CO2 Hydrogenation on Transition-Metal-Doped Cu(211) Surfaces.

The massive emission of CO2 has caused a series of environmental problems, including global warming, which exacerbates natural disasters and human health. Cu-based catalysts have shown great activity in the reduction of CO2, but the mechanism of CO2 activation remains ambiguous. In this work, we performed density functional theory (DFT) calculations to investigate the hydrogenation of CO2 on Cu(211)-Rh, Cu(211)-Ni, Cu(211)-Co, and Cu(211)-Ru surfaces. The doping of Rh, Ni, Co, and Ru was found to enhance CO2 hydrogenation to produce COOH. For CO2 hydrogenation to produce HCOO, Ru plays a positive role in promoting CO dissociation, while Rh, Ni, and Co increase the barriers. These results indicate that Ru is the most effective additive for CO2 reduction in Cu-based catalysts. In addition, the doping of Rh, Ni, Co, and Ru alters the electronic properties of Cu, and the activity of Cu-based catalysts was subsequently affected according to differential charge analysis. The analysis of Bader charge shows good predictions for CO2 reduction over Cu-based catalysts. This study provides some fundamental aids for the rational design of efficient and stable CO2-reducing agents to mitigate CO2 emission.

Cellulose Regeneration in Imidazolium-Based Ionic Liquids and Antisolvent Mixtures: A Density Functional Theory Study.

Cellulose can be dissolved in ionic liquids (ILs), and it can be recovered by adding antisolvent such as water or alcohol. In addition, the regenerated cellulose can be used for textiles, degradable membranes, hydrogels/aerogels, etc. However, the regenerated mechanism of cellulose remains ambiguous. In this work, density functional theory (DFT) calculation is reported for the cellulose regeneration from a cellulose/1-n-butyl-3-methylimidazolium acetate (BmimOAc)/water mixture. To investigate the microscopic effects of the antisolvents, we analyzed the structures and H-bonds of BmimOAc-nH2O and cellobiose-ILs-nH2O (n = 0-6) clusters. It can be found that when n ≥ 5 in the BmimOAc-nH2O clusters, the solvent-separated ion pairs (SIPs) play a dominant position in the system. With the increasing numbers of water molecules, the cation-anion interaction can be separated by water to reduce the effects of ILs on cellulose dissolution. Furthermore, the BmimOAc-nH2O and cellobiose-ILs (n = 0-6) clusters tend to be a more stable structure with high hydration in an aqueous solution. When the water molecules were added to the system, H-bonds can be formed among H2O, the hydroxyl of cellulose, and the oxygen of OAc. Therefore, the interactions between cellulose and ILs will be decreased to promote cellulose regeneration. This work would provide some help to understand the mechanism of cellulose regeneration from the view of theoretical calculation.

Fischer-Helferich glycosidation mechanism of glucose to methyl glycosides over Al-based catalysts in alcoholic media.

The Fischer-Helferich glycosidation reaction is generally the initial step in the conversion of glucose to levulinate in alcohol media. However, the relevant molecular mechanism catalyzed by Al-based catalysts is still not well understood. In this work, the reaction mechanism of the glycosidation from glucose to methyl glycosides catalyzed by Al3+ coordinated with methanol/methoxyl was investigated through density functional theory (DFT) calculations. The whole reaction process includes ring-opening, addition, and ring-closure events. The addition of methanol to the ring-opening structure of glucose makes the electronegativity of C1 site stronger to proceed with the following ring-closure reaction. Among the 28 kinds of ways of ring-closure reaction, the most preferred way is to close the loop through the six-membered ring (O5-C1) to generate methyl glucoside (MDGP). The rate-determining step is the ring-closure and the Al3+ shows a great catalytic effect which is mainly reflected in coordinating with the solvents to transfer protons. The results would be helpful to understanding the Fischer-Helferich glycosidation mechanism catalyzed by Al-based catalysts and comprehend the conversion of glucose to high value-added chemicals.

Probing the mechanism of the conversion of methyl levulinate into γ-valerolactone catalyzed by Al(OiPr)3 in an alcohol solvent: a DFT study.

Biomass-derived γ-valerolactone (GVL) is a versatile chemical that can be used in various fields. As an efficient, cheap, and sustainable catalyst, Al(OiPr)3 has been successfully used in the conversion of methyl levulinate (ML) to GVL in the solvent isopropanol (IPA). However, the molecular mechanism of this conversion catalyzed by Al(OiPr)3 remains ambiguous. To investigate the mechanism of the conversion of ML to GVL catalyzed by Al(OiPr)3, the reaction pathways, including the transesterification, Meerwein-Ponndorf-Verley (MPV) hydrogenation, and ring-closure steps, were probed using density functional theory (DFT) calculations at the M062X-D3/def2-TZVP level. Among the elementary steps, it is found that ring-closure is the rate-determining step and that Al3+ can coordinate with the oxygen of 2-hydroxy-isopropyl levulinate (2HIPL) to catalyze the last ring-closure step. A four-centered transition state can be formed, and Al(OiPr)3 shows a strong catalytic effect in the two steps of the ester exchange reaction. The center of Al(OiPr)3 mainly coordinates with the carbonyl oxygen atom of the ester to catalyze the reaction. The present study provides some help in understanding the conversion mechanism of ML to GVL and designing more effective catalysts for use in biomass conversion chemistry.

Selective Aerobic Oxidation of Csp3-H Bonds Catalyzed by Yeast-Derived Nitrogen, Phosphorus, and Oxygen Codoped Carbon Materials.

Nitrogen, phosphorus, and oxygen codoped carbon catalysts were successfully synthesized using dried yeast powder as a pyrolysis precursor. The yeast-derived heteroatom-doped carbon (yeast@C) catalysts exhibited outstanding performance in the oxidation of Csp3-H bonds to ketones and esters, giving excellent product yields (of up to 98% yield) without organic solvents at low O2 pressure (0.1 MPa). The catalytic oxidation protocol exhibited a broad range of substrates (38 examples) with good functional group tolerance, excellent regioselectivity, and synthetic utility. The yeast-derived heteroatom-doped carbon catalysts showed good reusability and stability after recycling six times without any significant loss of activity. Experimental results and DFT calculations proved the important role of N-oxide (N+-O-) on the surface of yeast@C and a reasonable carbon radical mechanism.

Theoretical Mechanism on the Cellulose Regeneration from a Cellulose/EmimOAc Mixture in Anti-Solvents.

The experiments on cellulose dissolution/regeneration have made some achievements to some extent, but the mechanism of cellulose regeneration in ionic liquids (ILs) and anti-solvent mixtures remains elusive. In this work, the cellulose regeneration mechanism in different anti-solvents, and at different temperatures and concentrations, has been studied with molecular dynamics (MD) simulations. The IL considered is 1-ethyl-3-methylimidazolium acetate (EmimOAc). In addition, to investigate the microcosmic effects of ILs and anti-solvents, EmimOAc-nH2O (n = 0-6) clusters have been optimized by Density Functional Theory (DFT) calculations. It can be found that water is beneficial to the regeneration of cellulose due to its strong polarity. The interactions between ILs and cellulose will become strong with the increase in temperature. The H-bonds of cellulose chains would increase with the rising concentrations of anti-solvents. The interaction energies between cellulose and the anions of ILs are stronger than that of cations. Furthermore, the anti-solvents possess a strong affinity for ILs, cation-anion pairs are dissociated to form H-bonds with anti-solvents, and the H-bonds between cellulose and ILs are destroyed to promote cellulose regeneration.

Mechanistic insight into the roles of anions and cations in the degradation of poly(ethylene terephthalate) catalyzed by ionic liquids.

Ionic liquids (ILs) have shown high catalytic activity in the degradation of poly(ethylene terephthalate) (PET), but the effects of the anions and cations, as well as the mechanism, remain ambiguous. Glycolysis is an important recycling method that converts waste PET into monomers through various chemical reactions. To reveal the role of ILs and the molecular mechanism of the glycolysis of PET, density functional theory (DFT) calculations have been carried out for the possible pathways for the generation of bis(hydroxyethyl)terephthalate (BHET) catalyzed by isolated anions/cations and ion pairs at different sites. The pathway with the lowest barrier for the glycolysis of PET is the cleavage of the C-O ester bond, which generates the BHET monomer. The synergistic effects of the cations and anions play a critical role in the glycolysis of PET. The cations mainly attack the carbonyl oxygen of PET to catalyze the reaction, and the anions mainly form strong H-bonds with PET and ethylene glycol (EG). In terms of the mechanism, the H-bonds render the hydroxyl oxygen of EG more electronegative. The cation coordinates the carbonyl oxygen of the ester, and the hydroxyl oxygen of EG attacks the ester group carbon of PET, with proton transfer to the carbonyl oxygen. A four-membered-ring transition state would be formed by PET, EG, and the IL catalyst, which regularly accelerates the degradation of PET. These results provide fundamental help in understanding the roles of ILs and the mechanism of IL-catalyzed PET degradation.

Theoretical study on the microscopic mechanism of lignin solubilization in Keggin-type polyoxometalate ionic liquids.

Keggin-type polyoxometalate derived ionic liquids (POM-ILs) have recently been presented as effective solvent systems for biomass delignification. To investigate the mechanism of lignin dissolution in POM-ILs, the system involving POM-IL ([C4C1Im]3[PW12O40]) and guaiacyl glycerol-ß-guaiacyl ether (GGE), which contains a ß-O-4 bond (the most dominant bond moiety in lignin), was studied using quantum mechanical calculations and molecular dynamics simulations. These studies show that more stable POM-IL structures are formed when [C4C1Im]+ is anchored in the connecting four terminal oxygen region of the [PW12O40]3- surface. The cations in POM-ILs appear to stabilize the geometry by offering strong and positively charged sites, and the POM anion is a good H-bond acceptor. Calculations of POM-IL interacting with GGE show the POM anion interacts strongly with GGE through many H-bonds and π-π interactions which are the main interactions between the POM-IL anion and GGE and are strong enough to force GGE into highly bent conformations. These simulations provide fundamental models of the dissolution mechanism of lignin by POM-IL, which is promoted by strong interactions of the POM-IL anion with lignin.

Theoretical studies on the noncovalent interaction of fructose and functionalized ionic liquids.

As a new kind of solvent and catalyst, the functionalized ionic liquids (ILs) had been successfully used in the conversion of fructose to high value-added biofuels. In this work, a detailed density functional theory (DFT) calculation had been carried out to investigate the interactions of fructose-ILs system. To study the effect of different anions and cations on the interaction with fructose, 25 different kinds of functionalized imidazolium-based ILs were calculated by using M06-2X-D3/6-311 + G** level. It was found that the interaction energies of fructose-anions were higher than those of the fructose-cations. The interaction will become stronger for the fructose and ILs when the alkyl chain of imidazolium-based cations was replaced with a functional group (COOH, OH or HSO3). However, when the length of the alkyl chain increased, it will result in a decrease in interaction energy due to the steric effect. In the anions (Y-SO3), the greater electronegativity of SO3 will lead to strong interaction with fructose. Also, this work simulates the interaction of fructose and ion pairs, with the results showing that hydrogen bonds (H-bonds) and π-stacking play an important role in the system. The present study provided basic aids to understand the structures and noncovalent interaction of fructose and functionalized ILs as well as the microscopic mechanism of fructose dissolution in the ILs.

Theoretical studies on glycolysis of poly(ethylene terephthalate) in ionic liquids.

Ionic liquids (ILs) present superior catalytic performance in the glycolysis of ethylene terephthalate (PET). To investigate the microscopic degradation mechanism of PET, density functional theory (DFT) calculations have been carried out for the interaction between ILs and dimer, which is considered to symbolize PET. We found that hydrogen bonds (H-bonds) play a critical role in the glycolysis process. In this study, 24 kinds of imidazolium-based and tertiary ammonium-based ILs were used to study the effect of different anions and cations on the interaction with PET. Natural bond orbital (NBO) analysis, atoms in molecules (AIM) and reduced density gradient (RDG) approaches were employed to make in-depth study of the nature of the interactions. It is concluded that the interaction of cations with dimer is weaker than that of anions and when the alkyl chain in the cations is replaced by an unsaturated hydrocarbon, the interaction will become stronger. Furthermore, anions play more important roles than cations in the actual interactions with dimer. When the hydrogen of methyl is replaced by hydroxyl or carboxyl, the interaction becomes weak for the amino acid anions and dimer. This work also investigates the interaction between dimer and ion pairs, with the results showing that anions play a key role in forming H-bonds, while cations mainly attack the oxygen of carbonyl and have a π-stacking interaction with dimer. The comprehensive mechanistic study will help researchers in the future to design an efficient ionic liquid catalyst and offer a better understanding of the mechanism of the degradation of PET.

P-N Conversion in a Water-Ionic Liquid Binary System for Nonredox Thermocapacitive Converters.

An intriguing p-n conversion of thermoelectric property was observed in a water-ionic liquid ([EMIm][Ac]) binary system with precise control over water content. The highest p-type and n-type Seebeck coefficient were optimized at water-[EMIm][Ac] molar ratio of 2:1 and 4:1, respectively. DFT calculation illustrates that a configuration of solvent separation ion pairs is preferred at the water-[EMIm][Ac] molar ratio of 4:1, leading to the p-n conversion through weakening interaction between anion clusters and gold electrodes. Furthermore, p-n thermocapacitive converters were integrated to enhance the output Seebeck voltages. This work opens up new perspectives for harvesting low grade heat with the use of fluidic materials.