Understanding the interaction properties of an eco-friendly corrosion inhibitor on Zn (1 1 0) surface: Comprehensive DFT-based MD simulation

Abstract Regarding the deleterious effects of corrosion for a wide range of metals and alloys, many different techniques have been developed to protect the metals against corrosion. Utilizing organic inhibitors, especially those that contain heteroatoms and multiple bonds has been found an effective approach. In this research, the adsorption of a novel green inhibitor, Laurhydrazide N′-propan-3-one (LHP), on the Zn (110) surface was investigated using dispersion corrected DFT calculations. Interaction energy and electronic structures were calculated for different orientations of the inhibitor toward the Zn surface. The validity of calculated interaction energy has been verified by the MP2 level of theory. The AIM theory analysis revealed that LHP bound strongly to the Zn surface through its O active site and also its orientation affects greatly the interaction energy. Furthermore, diffusion of LHP through its O atoms active sites was observed with the state-of-the-art DFT-MD simulation during the simulation procedure that agrees well with the experiments for similar molecules adsorbed on the metal surfaces. The presented findings afford a vital insight into the interactive nature of adsorbed inhibitors on metallic surfaces and will help to develop advanced functional materials in coating technologies.

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Bio-Templating: An Emerging Synthetic Technique for Catalysts. A Review

Catalysts ◽

10.3390/catal11111364 ◽

2021 ◽

Vol 11 (11) ◽

pp. 1364

Author(s):

M. Carmen Herrera-Beurnio ◽

Jesús Hidalgo-Carrillo ◽

Francisco J. López-Tenllado ◽

Juan Martin-Gómez ◽

Rafael C. Estévez ◽

...

Keyword(s):

Active Sites ◽

Experimental Studies ◽

Functional Materials ◽

Inorganic Materials ◽

Hierarchical Organization ◽

Materials Synthesis ◽

Energy Capture ◽

Wide Range ◽

Mineralization Processes ◽

And Storage

In the last few years, researchers have focused their attention on the synthesis of new catalyst structures based on or inspired by nature. Biotemplating involves the transfer of biological structures to inorganic materials through artificial mineralization processes. This approach offers the main advantage of allowing morphological control of the product, as a template with the desired morphology can be pre-determined, as long as it is found in nature. This way, natural evolution through millions of years can provide us with new synthetic pathways to develop some novel functional materials with advantageous properties, such as sophistication, miniaturization, hybridization, hierarchical organization, resistance, and adaptability to the required need. The field of application of these materials is very wide, covering nanomedicine, energy capture and storage, sensors, biocompatible materials, adsorbents, and catalysis. In the latter case, bio-inspired materials can be applied as catalysts requiring different types of active sites (i.e., redox, acidic, basic sites, or a combination of them) to a wide range of processes, including conventional thermal catalysis, photocatalysis, or electrocatalysis, among others. This review aims to cover current experimental studies in the field of biotemplating materials synthesis and their characterization, focusing on their application in heterogeneous catalysis.

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Assessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow

10.21203/rs.3.rs-396201/v1 ◽

2021 ◽

Author(s):

Hassan Aljama ◽

Martin Head-Gordon ◽

Alexis Bell

Keyword(s):

High Throughput ◽

High Throughput Screening ◽

Active Sites ◽

Density Functional ◽

Functional Materials ◽

No Adsorption ◽

Functional Theory ◽

Wide Range ◽

The Stability ◽

Shed Light

Abstract Cation exchanged-zeolites are functional materials with a wide range of applications from catalysis to sorbents. They present a challenge for computational studies using density functional theory due to the numerous possible active sites. From Al configuration, to placement of extra framework cation(s), to potentially different oxidation states of the cation, accounting for all these possibilities is not trivial. To make the number of calculations more tractable, most studies focus on a few active sites. We attempt to go beyond these limitations by implementing a workflow for a high throughput screening, designed to systematize the problem and exhaustively search for feasible active sites. We use Pd-exchanged CHA and BEA to illustrate the approach. After conducting thousands of individual calculations, we identify the sites most favorable for the Pd cation and discuss the results in detail. The high throughput screening identifies many energetically favorable sites that are non-trivial. Lastly, we employ these results to examine NO adsorption in Pd-exchanged CHA, which is a promising passive NOx adsorbent (PNA) during the cold start of automobiles. The results shed light on critical active sites for NOx capture that were not previously studied.

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Characterizing Bacterial Cellulose Produced byKomagataeibacter sucrofermentans H-110 on Molasses Medium and Obtaining a Biocomposite Based on It for the Adsorption of Fluoride

Polymers ◽

10.3390/polym13091422 ◽

2021 ◽

Vol 13 (9) ◽

pp. 1422

Author(s):

Viktor V. Revin ◽

Alexander V. Dolganov ◽

Elena V. Liyaskina ◽

Natalia B. Nazarova ◽

Anastasia V. Balandina ◽

...

Keyword(s):

Composite Material ◽

Adsorption Capacity ◽

Bacterial Cellulose ◽

Functional Materials ◽

Degree Of Crystallinity ◽

Maximum Adsorption Capacity ◽

Fluoride Ions ◽

Sorption Ability ◽

Wide Range ◽

Biocomposite Material

Currently, there is an increased demand for biodegradable materials in society due to growing environmental problems. Special attention is paid to bacterial cellulose, which, due to its unique properties, has great prospects for obtaining functional materials for a wide range of applications, including adsorbents. In this regard, the aim of this study was to obtain a biocomposite material with adsorption properties in relation to fluoride ions based on bacterial cellulose using a highly productive strain of Komagataeibacter sucrofermentans H-110 on molasses medium. Films of bacterial cellulose were obtained. Their structure and properties were investigated by FTIR spectroscopy, NMR, atomic force microscopy, scanning electron microscopy, and X-ray structural analysis. The results show that the fiber thickness of the bacterial cellulose formed by the K. sucrofermentans H-110 strain on molasses medium was 60–90 nm. The degree of crystallinity of bacterial cellulose formed on the medium was higher than on standard Hestrin and Schramm medium and amounted to 83.02%. A new biocomposite material was obtained based on bacterial cellulose chemically immobilized on its surface using atomic-layer deposition of nanosized aluminum oxide films. The composite material has high sorption ability to remove fluoride ions from an aqueous medium. The maximum adsorption capacity of the composite is 80.1 mg/g (F/composite). The obtained composite material has the highest adsorption capacity of fluoride from water in comparison with other sorbents. The results prove the potential of bacterial cellulose-based biocomposites as highly effective sorbents for fluoride.

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Advanced Functional Materials Based on Nanocellulose for Pharmaceutical/Medical Applications

Pharmaceutics ◽

10.3390/pharmaceutics13081125 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1125

Author(s):

Raluca Nicu ◽

Florin Ciolacu ◽

Diana E. Ciolacu

Keyword(s):

Rapid Development ◽

Cellulose Nanofibrils ◽

Functional Materials ◽

Medical Applications ◽

Bacterial Nanocellulose ◽

Green Materials ◽

Wide Range ◽

In Vivo Cytotoxicity

Nanocelluloses (NCs), with their remarkable characteristics, have proven to be one of the most promising “green” materials of our times and have received special attention from researchers in nanomaterials. A diversity of new functional materials with a wide range of biomedical applications has been designed based on the most desirable properties of NCs, such as biocompatibility, biodegradability, and their special physicochemical properties. In this context and under the pressure of rapid development of this field, it is imperative to synthesize the successes and the new requirements in a comprehensive review. The first part of this work provides a brief review of the characteristics of the NCs (cellulose nanocrystals—CNC, cellulose nanofibrils—CNF, and bacterial nanocellulose—BNC), as well as of the main functional materials based on NCs (hydrogels, nanogels, and nanocomposites). The second part presents an extensive review of research over the past five years on promising pharmaceutical and medical applications of nanocellulose-based materials, which have been discussed in three important areas: drug-delivery systems, materials for wound-healing applications, as well as tissue engineering. Finally, an in-depth assessment of the in vitro and in vivo cytotoxicity of NCs-based materials, as well as the challenges related to their biodegradability, is performed.

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NAD(P)H quinone oxidoreductase (NQO1): an enzyme which needs just enough mobility, in just the right places

Bioscience Reports ◽

10.1042/bsr20180459 ◽

2019 ◽

Vol 39 (1) ◽

Cited By ~ 14

Author(s):

Angel L. Pey ◽

Clare F. Megarity ◽

David J. Timson

Keyword(s):

Active Sites ◽

Physiological Role ◽

Polymorphic Form ◽

Normal Function ◽

Enzyme Mechanism ◽

Quinone Oxidoreductase ◽

Lower Stability ◽

Increased Risk ◽

Wide Range ◽

The Right

AbstractNAD(P)H quinone oxidoreductase 1 (NQO1) catalyses the two electron reduction of quinones and a wide range of other organic compounds. Its physiological role is believed to be partly the reduction of free radical load in cells and the detoxification of xenobiotics. It also has non-enzymatic functions stabilising a number of cellular regulators including p53. Functionally, NQO1 is a homodimer with two active sites formed from residues from both polypeptide chains. Catalysis proceeds via a substituted enzyme mechanism involving a tightly bound FAD cofactor. Dicoumarol and some structurally related compounds act as competitive inhibitors of NQO1. There is some evidence for negative cooperativity in quinine oxidoreductases which is most likely to be mediated at least in part by alterations to the mobility of the protein. Human NQO1 is implicated in cancer. It is often over-expressed in cancer cells and as such is considered as a possible drug target. Interestingly, a common polymorphic form of human NQO1, p.P187S, is associated with an increased risk of several forms of cancer. This variant has much lower activity than the wild-type, primarily due to its substantially reduced affinity for FAD which results from lower stability. This lower stability results from inappropriate mobility of key parts of the protein. Thus, NQO1 relies on correct mobility for normal function, but inappropriate mobility results in dysfunction and may cause disease.

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A Zirconium Metal-Organic Framework with SOC Topological Net for Catalytic Peptide Bond Hydrolysis

10.26434/chemrxiv.14472681.v1 ◽

2021 ◽

Author(s):

Sujing Wang ◽

Antoine Tissot ◽

Guillaume Maurin ◽

Tatjana Parac-Vogt ◽

Christian Serre ◽

...

Keyword(s):

Active Sites ◽

Metal Organic Framework ◽

Cost Effective ◽

Peptide Bond ◽

Catalytic Performance ◽

Wide Range ◽

Horse Heart Myoglobin ◽

Metal Organic ◽

Effective Synthesis ◽

Organic Framework

<div>The discovery of nanozymes for selective cleavage of proteins would boost the emerging areas of modern proteomics, however, the development of efficient and reusable artificial catalysts for peptide bond hydrolysis is challenging. Here we report the detailed catalytic properties of a microporous zirconium carboxylate metal-organic framework, MIP-201, in promoting peptide bond hydrolysis in a simple dipeptide, as well as in horse-heart myoglobin (Mb) protein that consists of 153 amino acids. We demonstrate that MIP-201 features an excellent catalytic activity and selectivity, a good tolerance toward reaction conditions covering a wide range of different pH values, and importantly, an exceptional recycling ability associated with easy regeneration process. Taking into account the excellent catalytic performance of MIP-201 and its other advantages such as 6-connected Zr6 cluster active sites, the green, scalable and cost-effective synthesis, and an outstanding chemical and architectural stability, our finding suggests that MIP-201 may be a promising and practical alternative to the current commercially available catalysts for peptide bond hydrolysis.</div>

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A Zirconium Metal-Organic Framework with SOC Topological Net for Catalytic Peptide Bond Hydrolysis

10.26434/chemrxiv.14472681 ◽

2021 ◽

Author(s):

Sujing Wang ◽

Antoine Tissot ◽

Guillaume Maurin ◽

Tatjana Parac-Vogt ◽

Christian Serre ◽

...

Keyword(s):

Active Sites ◽

Metal Organic Framework ◽

Cost Effective ◽

Peptide Bond ◽

Catalytic Performance ◽

Wide Range ◽

Horse Heart Myoglobin ◽

Metal Organic ◽

Effective Synthesis ◽

Organic Framework

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Proton Pumping and Non-Pumping Terminal Respiratory Oxidases: Active Sites Intermediates of These Molecular Machines and Their Derivatives

International Journal of Molecular Sciences ◽

10.3390/ijms221910852 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10852

Author(s):

Sergey A. Siletsky ◽

Vitaliy B. Borisov

Keyword(s):

Active Sites ◽

Three Dimensional ◽

Molecular Machines ◽

Proton Pumping ◽

Stress Reactions ◽

Low Oxygen ◽

Functional Studies ◽

Wide Range ◽

Regulatory Cascades ◽

Respiratory Oxidases

Terminal respiratory oxidases are highly efficient molecular machines. These most important bioenergetic membrane enzymes transform the energy of chemical bonds released during the transfer of electrons along the respiratory chains of eukaryotes and prokaryotes from cytochromes or quinols to molecular oxygen into a transmembrane proton gradient. They participate in regulatory cascades and physiological anti-stress reactions in multicellular organisms. They also allow microorganisms to adapt to low-oxygen conditions, survive in chemically aggressive environments and acquire antibiotic resistance. To date, three-dimensional structures with atomic resolution of members of all major groups of terminal respiratory oxidases, heme-copper oxidases, and bd-type cytochromes, have been obtained. These groups of enzymes have different origins and a wide range of functional significance in cells. At the same time, all of them are united by a catalytic reaction of four-electron reduction in oxygen into water which proceeds without the formation and release of potentially dangerous ROS from active sites. The review analyzes recent structural and functional studies of oxygen reduction intermediates in the active sites of terminal respiratory oxidases, the features of catalytic cycles, and the properties of the active sites of these enzymes.

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A Comprehensive In Silico Perspective For Discovery of Novel Inhibitory Candidates Targeting Versatile Transcriptional Repressor MBD2

10.21203/rs.3.rs-578382/v2 ◽

2021 ◽

Author(s):

Zihni Onur Çalışkaner

Keyword(s):

Dna Methylation ◽

Cancer Progression ◽

Md Simulation ◽

Dna Interaction ◽

Binding Energies ◽

Epigenetic Mechanism ◽

Energy Decomposition ◽

Computational Docking ◽

Somatic Cell Reprogramming ◽

Wide Range

Abstract Genome methylation is a key epigenetic mechanism in various biological events such as development, cellular differentiation, cancer progression, aging, and iPSC reprogramming. Crosstalk between DNA methylation and regulation in gene expression is employed through MBD2, known as reader of DNA methylation and suggested as a drug target. Despite its magnitude of significance and rationale of nomination, a scarcely limited number of druggable ligands has been detected so far. Hence, we screened a comprehensive compound library, and then certain of them were subjected to computational docking analysis by targeting the methylated DNA-binding domain of human MBD2. We could detect reasonable binding energies and docking residues presumably located in druggable pockets. Docking results were also validated via MD simulation and per-residue energy decomposition calculation. Drug-likeness of tested ligands was assessed through ADMET prediction in order to foresee off-target side effects for future studies. Herein, on the basis of collaborating approaches such as molecular docking, MD simulation, energy decomposition, and ADMET prediction, notably two compounds named CID3100583 and 8,8-Ethylenebistheophylline, have become prominent as novel candidates, possibly disrupting MBD2MBD–DNA interaction. Hereby, these compounds exhibit a promising usage potential in a wide range of implementations from cancer treatment to somatic cell reprogramming protocols.

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A ladder coordination polymer based on Ca2+and (4,5-dicyano-1,2-phenylene)bis(phosphonic acid): crystal structure and solution-state NMR study

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229616012328 ◽

2016 ◽

Vol 72 (9) ◽

pp. 685-691

Author(s):

Nutalapati Venkatramaiah ◽

Ricardo F. Mendes ◽

Artur M. S. Silva ◽

João P. C. Tomé ◽

Filipe A. Almeida Paz

Keyword(s):

Crystal Structure ◽

Coordination Polymer ◽

Phosphonic Acid ◽

Cyano Group ◽

Functional Materials ◽

One Dimensional ◽

Solution State ◽

Nmr Study ◽

Wide Range ◽

Organic Linker

The preparation of coordination polymers (CPs) based on either transition metal centres or rare-earth cations has grown considerably in recent decades. The different coordination chemistry of these metals allied to the use of a large variety of organic linkers has led to an amazing structural diversity. Most of these compounds are based on carboxylic acids or nitrogen-containing ligands. More recently, a wide range of molecules containing phosphonic acid groups have been reported. For the particular case of Ca2+-based CPs, some interesting functional materials have been reported. A novel one-dimensional Ca2+-based coordination polymer with a new organic linker, namely poly[[diaqua[μ4-(4,5-dicyano-1,2-phenylene)bis(phosphonato)][μ3-(4,5-dicyano-1,2-phenylene)bis(phosphonato)]dicalcium(II)] tetrahydrate], {[Ca2(C8H4N2O6P2)2(H2O)2]·4H2O}n, has been prepared at ambient temperature. The crystal structure features one-dimensional ladder-like∞1[Ca2(H2cpp)2(H2O)2] polymers [H2cpp is (4,5-dicyano-1,2-phenylene)bis(phosphonate)], which are created by two distinct coordination modes of the anionic H2cpp2−cyanophosphonate organic linkers: while one molecule is only bound to Ca2+cationsviathe phosphonate groups, the other establishes an extra single connectionviaa cyano group. Ladders close pack with water molecules through an extensive network of strong and highly directional O—H...O and O—H...N hydrogen bonds; the observed donor–acceptor distances range from 2.499 (5) to 3.004 (6) Å and the interaction angles were found in the range 135–178°. One water molecule was found to be disordered over three distinct crystallographic positions. A detailed solution-state NMR study of the organic linker is also provided.

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