free-energy

The electrochemical reduction of CO2 is an efficient channel to facilitate energy conversion, but the rapid design and rational screening of high-performance catalysts remain a great challenge. In this work, we investigated the relationships between the configuration, energy, and electronic properties of SnS2 loaded with transition metal single atom (TM@SnS2 ) and analyzed the mechanism of CO2 activation and reduction by using density functional theory. The "charge transfer bridge" promoted the adsorption of CO2 on TM@SnS2 , thus enhancing the binding of HCOOH∗ to the catalyst for further hydrogenation and reduction to high-value CH4 ...

The adsorption mechanisms of CO2 on macroporous cation exchange resin (MCER), D001 ion-exchange resin, and macroporous ion-exchange resin organic amine composite materials (MCER-DEA and D001-PEI) were studied by density functional theory (DFT). The adsorption energies and Mulliken atomic charges in the adsorption process were analyzed, indicating that CO2 on MCER and D001 were physisorbed. The adsorption heat of the adsorption process of MCER-DEA and D001-PEI was calculated by the Monte Carlo method, and it was found that the adsorption process of CO2 by MCER-DEA and D001-PEI was both physical adsorption and chemical adsorption...

Flavor esters are organic compounds widely used in the food industry to enhance the aroma and taste of products. However, most chemical processes for the production of these flavoring compounds use toxic organic solvents. Some organic solvents derived from petroleum can leave behind residual traces in food products, which may raise concerns about potential health risks and contamination. In this study, we employ Eversa Transform 2.0, a commercial lipase derived from the lipase from Thermomyces lanuginosus , to produce geranyl butyrate in aqueous media...

Metal corrosion has recently emerged as a growing concern, impacting both local and industrial operations and disrupting conventional production methods. The utilization of green inhibitors to mitigate the metal degradation has garnered extensive attention from researchers and industrial professionals due to their prominent advantages: high efficiency, cost-effectiveness, and eco-friendliness. A novel ecofriendly inhibitor was prepared from Praecitrullus fistulosus (tinda fruit and peel) for mild steel (MS) corrosion in 1 M HCl...

Non-equilibrium (NEQ) alchemical free energy calculations are an emerging tool for accurately predicting changes in protein folding free energy resulting from amino acid mutations. In this study, this method in combination with the Rosetta ddg monomer tool was applied to predict more thermostable variants of the polyethylene terephthalate (PET) degrading enzyme DuraPETase. The Rosetta ddg monomer tool efficiently enriched promising mutations prior to more accurate prediction by NEQ alchemical free energy calculations...

Global sustainable development faces a significant challenge in effectively utilizing CO2 . Meanwhile, CO2 biological fixation offers a promising solution. CO2 has the highest oxidation state (+4 valence state), whereas typical multi‑carbon chemicals have lower valence states. The Gibbs free energy (ΔG) changes of CO2 reductive reactions are generally positive and this renders it necessary to input different forms of energy. Although biological carbon fixation processes are friendly to operate, the thermodynamic obstacles must be overcome...

Type 2 diabetes mellitus (T2DM) has become a serious public health problem both in our country and worldwide, being the most prevalent type of diabetes. The combined use of drugs in the treatment of T2DM leads to serious side effects, including gastrointestinal problems, liver toxicity, hypoglycemia, and treatment costs. Hence, there has been a growing emphasis on drugs that demonstrate dual interactions. Several studies have suggested that dual-target agents for peroxisome proliferator-activated receptor-γ (PPAR-γ) and alpha-glucosidase (α-glucosidase) could be a potent approach for treating patients with diabetes...

The pigmentation of the skin, modulated by different actors in melanogenesis, is mainly due to the melanins (protective pigments). In humans, these pigments' precursors are synthetized by an enzyme known as tyrosinase (TyH). The regulation of the enzyme activity by specific modulators (inhibitors or activators) can offer a means to fight hypo- and hyper-pigmentations responsible for medical, psychological and societal handicaps. Herein, we report the investigation of phenylalanine derivatives as TyH modulators...

HYPOTHESIS: Graphene quantum dots (GQDs) with various functional groups are hypothesized to inhibit the α-synuclein (αS) dimerization, a crucial step in Parkinson's disease pathogenesis. The potential of differently functionalized GQDs is systematically explored. EXPERIMENTS: All-atom replica-exchange molecular dynamics simulations (accumulating to 75.6 μs) in explicit water were performed to study the dimerization of the αS non-amyloid component region and the influence of GQDs modified with various functional groups...

The kinesin-5 family member, Eg5, plays very important role in the mitosis. As a mitotic protein, Eg5 is the target of various mitotic inhibitors. There are two targeting pockets in the motor domain of Eg5, which locates in the α2/L5/α3 region and the α4/α6 region respectively. We investigated the interactions between the different inhibitors and the two binding pockets of Eg5 by using all-atom molecular dynamics method. Combined the conformational analysis with the free-energy calculation, the binding patterns of inhibitors to the two binding pockets are shown...

Single atom metal-nitrogen-carbon materials have emerged as remarkably potent catalysts, demonstrating unprecedented potential for the photo-driven reduction of CO2 . Herein, a unique Cu@g-C3 N5 catalyst obtained by cooperation of single atom Cu and nitrogen-rich g-C3 N5 is proposed. The particular CuN diatomic active sites (DAS) in Cu@g-C3 N5 contribute to the formation of highly stable CuOCN adsorption, a key configuration for CO2 activation and CC coupling. The synergistic diatomic active sites interaction is found responsible for the efficient photoreduction of CO2 to C2 H4 which has been demonstrated in our Gibbs free energy calculation and COHP analysis...

We used umbrella sampling and the milestoning simulation method to study the dissociation of multiple ligands from protein kinase PYK2. The activation barriers obtained from the potential of mean force of the umbrella sampling simulations correlated well with the experimental dissociation rates. Using the zero-temperature string method, we obtained optimized paths along the free-energy surfaces for milestoning simulations of three ligands with a similar structure. The milestoning simulations gave an absolute dissociation rate within 2 orders of magnitude of the experimental value for two ligands but at least 3 orders of magnitude too high for the third...

Double decoupling absolute binding free energy simulations require an intermediate state at which the ligand is held solely by restraints in a position and orientation resembling the bound state. One possible choice consists of one distance, two angle, and three dihedral angle restraints. Here, I demonstrate that in practically all cases the analytical correction derived under the rigid rotator harmonic oscillator approximation is sufficient to account for the free energy of the restraints.

Identification of stereo- and positional isomers detected with high-resolution mass spectrometry (HRMS) is often challenging due to near-identical fragmentation spectra (MS2 ), similar retention times, and collision cross-section values (CCS). Here we address this challenge on the example of hydroxylated polychlorinated biphenyls (OH-PCBs) with the aim to (1) distinguish between isomers of OH-PCBs using two-dimensional ion mobility spectrometry (2D-IMS) and (2) investigate the structure of the fragments of OH-PCBs and their fragmentation mechanisms by ion mobility spectrometry coupled to high-resolution mass spectrometry (IMS-HRMS)...

The formation of pores over lipid membranes by the application of electric fields, termed membrane electroporation, is widely used in biotechnology and medicine to deliver drugs, vaccines, or genes into living cells. Continuum models for describing the free energy landscape of membrane electroporation were proposed decades ago, but they have never been tested against spatially detailed atomistic models. Using molecular dynamics (MD) simulations with a recently proposed reaction coordinate, we computed potentials of mean force of pore nucleation and pore expansion in lipid membranes at various transmembrane potentials...

This paper sheds light on the meaning of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) data. HDX-MS data provide not structural information but dynamic information on an analyte protein. First, the reaction mechanism of backbone amide HDX reaction is considered and the correlation between the parameters from an X-ray crystal structure and the protection factors of HDX reactions of cytochrome c is evaluated. The presence of H-bonds in a protein structure has a strong influence on HDX rates which represent protein dynamics, while the solvent accessibility only weakly affects the HDX rates...

Due to the superior catalytic activity and efficient utilization of noble metals, nanocatalysts are extensively used in the modern industrial production of chemicals. The surface structures of these materials are significantly influenced by reactive adsorbates, leading to dynamic behavior under experimental conditions. The dynamic nature poses significant challenges in studying the  structure-activity relations of catalysts. Herein, we unveil an anomalous entropic effect on catalysis via surface pre-melting of nanoclusters through machine learning accelerated molecular dynamics and free energy calculation...

Acylphosphatase (AcP) is an enzyme which catalyses the hydrolysis of acylphosphate. The binding with the phosphate ion (Pi) assumes significance in preserving both the stability and enzymatic activity of AcP. While previous studies using single molecule force spectroscopy explored the mechanical properties of AcP, the influence of Pi on its folding and unfolding dynamic behaviors remains unexplored. In this work, using stable magnetic tweezers, we measured and compared the force-dependent folding and unfolding rates of AcP in the Tris buffer and phosphate buffer within a force range from 2 pN to 40 pN...

Although the atmospheric stability of lead-free inorganic double perovskite (DP) solar cells (PSCs) looks promising, their further development is hampered by inadequate film quality and non-radiative carrier recombination at the interfaces. Herein, the incorporation of a newly developed intriguing class of 2D material Ti3 C2 Tx MXene nanosheets with the photo-absorbing Cu2 AgBiI6 (CABI) active layer of a fully inorganic solar cell is reported. The highly conductive Ti3 C2 Tx nanosheets work as a multi-functional additive by tuning the band gap, reducing the non-radiative carrier recombination, and inhibiting carrier accumulation...

Breast cancer is still the largest cause of cancer death in women, and around 70% of primary breast cancer patients are estrogen receptor (ER)-positive, which is the most frequent kind of breast cancer. The lemur tyrosine kinase-3 (LMTK3) receptor has been linked to estrogen responsiveness in breast cancer. However, the function of LMTK3 in reaction to cytotoxic chemotherapy has yet to be studied. Breast cancer therapy research remains tricky due to a paucity of structural investigations on LMTK3. We performed structural investigations on LMTK3 using molecular docking and molecular dynamics (MD) simulations of the LMTK3 receptor in complex with the top three inhibitor molecules along with a control inhibitor...