Theoretical and Experimental Study on Carbodiimide Formation.

Carbodiimides are important crosslinkers in organic synthesis and are used in the isocyanate industry as modifier additives. Therefore, the understanding of their formation is of high importance. In this work, we present a theoretical B3LYP/6-31G(d) and SMD solvent model and experimental investigation of the formation of diphenylcarbodiimide (CDI) from phenyl isocyanate using a phosphorus-based catalyst (MPPO) in ortho-dichlorobenzene (ODCB) solvent. Kinetic experiments were based on the volumetric quantitation of CO2 evolved, at different temperatures between 40 and 80 °C. Based on DFT calculations, we managed to construct a more detailed reaction mechanism compared to previous studies which is supported by experimental results. DFT calculations revealed that the mechanism is composed of two main parts, and the rate determining step of the first part, controlling the CO2 formation, is the first transition state with a 52.9 kJ mol-1 enthalpy barrier. The experimental activation energy was obtained from the Arrhenius plot (ln k vs. 1/T) using the observed second-order kinetics, and the obtained 55.8 ± 2.1 kJ mol-1 was in excellent agreement with the computational one, validating the complete mechanism, giving a better understanding of carbodiimide production from isocyanates.

Effect of applying carbodiimide combined with a two-step self-etch adhesive durability.

BACKGROUND: This study investigated the effect of carbodiimide (EDC) combined with Clearfil SE self-etch adhesive on the shear bond strength (SBS), crosslinking degree, denaturation temperature, and enzyme activity of dentin in vitro. MATERIALS AND METHODS: Collected human sound third molars were randomly divided into different groups with or without EDC treatment (0.01-1 M). The specimens (n = 16)were stored for 24 h (immediate) or 12 months (aging) before testing the SBS. Fine dentin powder was obtained and treated with the same solutions. Then the crosslinking degree, denaturation temperature (Td), and enzyme activity were tested. Statistical analysis was performed using a one-way analysis of variance (ANOVA) to compare the differences of data between groups (α = 0.05). RESULTS: There was a significant drop in immediate SBS and more adhesive fracture of 1.0 M EDC group, while there were no significant differences among the other groups. SEM showed a homogeneous interface under all treatments. After 12 months of aging, the SBS significantly decreased. Less decreases of SBS in the 0.3 and 0.5 M groups were found. Due to thermal and enzymatical properties consideration, the 0.3 and 0.5 M treatments also showed higher cross-link degree and Td with lower enzyme activity. CONCLUSION: 0.3 and 0.5 M EDC may be favorable for delaying the aging of self-etch bond strength for 12 months. But it is still needed thoroughly study.

Synthesis of the Antimicrobial Peptide Murepavadin Using Novel Coupling Agents.

The problem of antimicrobial resistance is becoming a daunting challenge for human society and healthcare systems around the world. Hence, there is a constant need to develop new antibiotics to fight resistant bacteria, among other important social and economic measures. In this regard, murepavadin is a cyclic antibacterial peptide in development. The synthesis of murepavadin was undertaken in order to optimize the preparative protocol and scale-up, in particular, the use of new activation reagents. In our hands, classical approaches using carbodiimide/hydroxybenzotriazole rendered low yields. The use of novel carbodiimide and reagents based on OxymaPure® and Oxy-B is discussed together with the proper use of chromatographic conditions for the adequate characterization of peptide crudes. Higher yields and purities were obtained. Finally, the antimicrobial activity of different synthetic batches was tested in three Pseudomonas aeruginosa strains, including highly resistant ones. All murepavadin batches yielded the same highly active MIC values and proved that the chiral integrity of the molecule was preserved throughout the whole synthetic procedure.

The Influence of Various Crosslinking Conditions of EDC/NHS on the Properties of Fish Collagen Film.

The process of crosslinking improves the physicochemical properties of biopolymer-based composites, making them valuable for biomedical applications. EDC/NHS-crosslinked collagen materials have a significant potential for tissue engineering applications, due to their enhanced properties and biocompatibility. Chemical crosslinking of samples can be carried out in several ways, which is crucial and has a direct effect on the final properties of the obtained material. In this study, the effect of crosslinking conditions on the properties of collagen films using EDC and NHS was investigated. Studies included FTIR spectroscopy, AFM, swelling and degradation tests, mechanical testing and contact angle measurements. Evaluation of prepared collagen films indicated that both crosslinking agents and crosslinking conditions influenced film properties. Notable alternations were observed in the infrared spectrum of the sample, to which EDC was added directly to the fish collagen solution. The same sample indicated the lowest Young modulus, tensile strength and breaking force parameters and the highest elongation at break. All samples reached the maximum swelling degree two hours after immersion in PBS solution; however, the immersion-crosslinked samples exhibited a significantly lower degree of swelling and were highly durable. The highest roughness was observed for the collagen film crosslinked with EDC, whereas the lowest was observed for the specimen crosslinked with EDC with NHS addition. The crosslinking agents increased the surface roughness of the collagen film, except for the sample modified with the addition of EDC and NHS mixture. All films were characterized by hydrophilic character. The films' modification resulted in a decrease in their hydrophilicity and wettability. Our research allows for a comparison of proposed EDC/NHS crosslinking conditions and their influence on the physicochemical properties of fish collagen thin films. EDC and NHS are promising crosslinking agents for the modification of fish collagen used in biomedical applications.

A Comparative Study of the Effects of Different Crosslinking Methods on the Physicochemical Properties of Collagen Multifilament Bundles.

Crosslinking is usually required to improve the mechanical properties and stability of collagen-based scaffolds. Introducing exogenous crosslinks into collagen may however affect the collagen structure. Since the architecture of collagen is tied to its functionality, it is important to study the effect of crosslinking and to select a crosslinking method that preserves both the collagen structure and mechanical properties. The objective of this study is to compare the effect of various crosslinking methods on the structure and mechanical properties of bioartificial tendon-like materials (collagen multifilament bundles) fabricated by contact drawing. We examine both physical (ultraviolet light, UVC) and chemical (genipin, carbodiimide (EDC), and glutaraldehyde) crosslinking methods. The presence of collagen and the formation of well-ordered collagen structures are confirmed by attenuated total reflectance Fourier-transform infrared spectromicroscopy and wide-angle X-ray scattering for all crosslinking methods. The morphology of the collagen multifilament bundles is similar across crosslinking methods. Swelling of the multifilament bundles is dramatically reduced following crosslinking and varies by crosslinking method, with genipin- and carbodiimide-crosslinked specimens swelling the least. Ultimate tensile strength (UTS) and Young's modulus significantly improve for all crosslinked specimens compared to non-crosslinked specimens. Glutaraldehyde crosslinked collagen multifilament bundles display the highest UTS values ranging from 33.82±0.0 MPa to 45.59±0.76 MPa.

A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS.

A key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing the structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. Although dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at adenine (A) and cytosine (C) at neutral pH. The reagent 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) was recently shown to modify the WC face of guanine (G) and uracil (U). Although useful at lower concentrations in experiments that measure chemical modifications by reverse transcription (RT) stops, at higher concentrations necessary for detection by mutational profiling (MaP), EDC treatment leads to degradation of RNA. Here, we demonstrate EDC-stimulated degradation of RNA in Gram-negative and Gram-positive bacteria. In an attempt to overcome these limitations, we developed a new carbodiimide reagent, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide methiodide (ETC), which we show specifically modifies unpaired Gs and Us in vivo without substantial degradation of RNA. We establish ETC as a probe for MaP and optimize the RT conditions and computational analysis in Escherichia coli Importantly, we demonstrate the utility of ETC as a probe for improving RNA structure prediction both alone and with DMS.

The effect of carbodiimide on push-out bond strength of fiber posts and endogenous enzymatic activity.

BACKGROUND: To investigate the effect of 0.3 M 1-ethyl-3(3-dimethylaminopropyl) carbodiimide (EDC) aqueous solution pretreatment on push-out bond strength (PBS) and matrix-metalloproteinases (MMPs) activity within radicular dentin when different post cementation strategies were employed. METHODS: One hundred and twenty monoradicular human teeth were endodontically treated and randomly divided into six groups, depending on the cementation strategy and root dentin pretreatment (n = 20): EAR: cementation with an etch-and-rinse adhesive (LuxaBond Total Etch, DMG) and resin cement (LuxaCore Z Dual, DMG); EAR/EDC: 1 min EDC pretreatment after etching + EAR; SE: cementation with a self-etch primer (Multilink Primer, Ivoclar Vivadent) and corresponding cement (Multilink Automix, Ivoclar Vivadent); SE/EDC: self-etch primer + EDC pretreatment + SE; SA: cementation with a universal self-adhesive cement (RelyX Universal, 3 M); SA/EDC: EDC pretreatment + SA. Slices were submitted to PBS test and interfacial nanoleakage evaluation 24 h after cementation or after thermocycling (40.000 cycles, 5-55 °C). To investigate the effect of EDC on MMPs activity, 4 additional first maxillary premolars per group were processed for in situ zymography analysis. Multivariate ANOVA and post hoc Tukey tests were used to analyze PBS values. The data from in situ zymography were analyzed with Kruskal-Wallis test and Dunn's pairwise multiple comparison procedures (α = 0.05). RESULTS: The variables "EDC pretreatment", "root region" and "thermocycling" significantly influenced PBS (p < 0.05), while the variable "cementation strategy" had no influence (p > 0.05). Thermocycling significantly reduced PBS in SE and SA groups (p < 0.05). EDC was effective in preserving PBS after artificial aging. EDC pretreatment significantly reduced enzymatic activity at baseline in EAR and SE groups, and in SA group after thermocycling (p < 0.05). CONCLUSIONS: The use of EDC prevents the reduction of bond-strength values after artificial aging and silences endogenous enzymatic activity within radicular dentin when different cementation strategies were employed.

Chemical modification of acellular fish skin as a promising biological scaffold by carbodiimide cross-linker for wound healing.

Biological matrices can be modified with cross-linkers to improve some of their characteristics as scaffolds for tissue engineering. In this study, chemical cross-linker 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) was used with different ratios (5, 10, 20, 30, and 40 mM) to improve properties such as mechanical strength, denaturation temperature, and degradability of the acellular fish skin as a biological scaffold for tissue engineering applications. Morphological analysis showed that the use of cross-linker at low concentrations had no effect on the structure and textiles of the scaffold, while increasing mechanical strength, denaturation temperature, and degradation time. Cytotoxicity and cellular studies showed that the optimal cross-linker concentration did not significantly affect cell viability as well as cell adhesion. In general, utilising the carbodiimide cross-linker with the optimal ratio can improve the characteristics and function of the biological tissues such as acellular fish skin.

An Iodide-Mediated Anodic Amide Coupling.

The ubiquity of amide bonds, present in natural products and common pharmaceuticals renders this functional group one of the most prevalent in organic chemistry. Despite its importance and a wide variety of existing methods for its formation, the latter still can be a challenge for classical activating reagents such as chloridating agents or carbodiimides. As the spent reagents often cannot be recycled, the development of more sustainable methods is highly desirable. Herein, we report an operationally simple and mild indirect electrochemical protocol to effect the condensation of carboxylic acids with amines, forming a wide variety of carboxamides.

A comprehensive review on methods for promotion of mechanical features and biodegradation rate in amniotic membrane scaffolds.

Amniotic membrane (AM) is a biological tissue that surrounds the fetus in the mother's womb. It has pluripotent cells, immune modulators, collagen, cytokines with anti-fibrotic and anti-inflammatory effect, matrix proteins, and growth factors. In spite of the biological characteristics, some results have been released in preventing the adhesion on traumatized surfaces. Application of the AM as a scaffold is limited due to its low biomechanical resistance and rapid biodegradation. Therefore, for using the AM during surgery, its modification by different methods such as cross-linking of the membrane collagen is necessary, because the cross-linking is an effective way to reduce the rate of biodegradation of the biological materials. In addition, their cross-linking is likely an efficient way to increase the tensile properties of the material, so that they can be easily handled or sutured. In this regard, various methods related to cross-linking of the AM subsuming the composite materials, physical cross-linking, and chemical cross-linking with the glutraldehyde, carbodiimide, genipin, aluminum sulfate, etc. are reviewed along with its advantages and disadvantages in the current work.

pH-regulated interaction modes between cyanidin-3-glucoside and phenylboronic acid-modified alginate.

Stabilizing mechanisms through covalent and non-covalent interactions have been studied along the years for color stabilization of anthocyanin dyes. In this work, the chemical functionalization of a natural and biocompatible marine-based polysaccharide (alginic acid) with 3-aminophenylboronic acid via carbodiimide coupling chemistry was carried out in order to create a bifunctional material for pH-dependent selective interaction with colored cyanidin-3-glucoside chemical species. The interaction studies were performed by UV-Vis, 1H, and 11B NMR spectroscopy. Overall, the apparent acidic and hydration constants are more stabilized in the presence of phenylboronic acid-modified alginate. For more acidic pH values the red cationic flavylium cation of cyanidin-3-glucoside mainly interacts through non-covalent electrostatic interactions with the carboxylate groups of the biopolymer derivative with association constant around 0.5 mM-1 while at higher pH values boronate-catechol covalent bonds are favored, promoting the stabilization of the colored neutral and anionic quinoidal bases of anthocyanins instead of colorless hemiketal and chalcones.

Amination of 5-Spiro-Substituted 3-Hydroxy-1,5-dihydro-2H-pyrrol-2-ones.

The 3-hydroxy-1,5-dihydro-2H-pyrrol-2-one motif is a valuable scaffold in drug discovery. The replacement of the 3-oxy fragment in 3-hydroxy-1,5-dihydro-2H-pyrrol-2-ones-based compounds with a 3-amino one (3-amino analogs of 3-hydroxy-1,5-dihydro-2H-pyrrol-2-ones, 3-amino-1,5-dihydro-2H-pyrrol-2-ones) can play a crucial role in their biological effect. Thus, approaches to 3-amino-1,5-dihydro-2H-pyrrol-2-ones are of significant interest. We developed an approach to 5-spiro-substituted 3-amino-1,5-dihydro-2H-pyrrol-2-ones that could not be obtained using previously reported approaches (reactions of 3-hydroxy-1,5-dihydro-2H-pyrrol-2-ones with amines). The developed approach is based on the thermal decomposition of 1,3-disubstituted urea derivatives of 5-spiro-substituted 3-hydroxy-1,5-dihydro-2H-pyrrol-2-ones, which were prepared via their reaction with carbodiimides.

A rapid lateral flow immunoassay strip for detection of SARS-CoV-2 antigen using latex microspheres.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious and concealed virus that causes pneumonia, severe acute respiratory syndrome, and even death. Although the epidemic has been controlled since the development of vaccines and quarantine measures, many people are still infected, particularly in third-world countries. Several methods have been developed for detection of SARS-CoV-2, but owing to its price and efficiency, the immune strip could be a better method for the third-world countries. METHODS: In this study, two antibodies were linked to latex microspheres, using 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide, as the bridge to decrease the cost further and improve the detection performance. The specificity of the lateral flow immunoassay strip (LFIA) was tested by several common viruses and respiratory bacterial infections. Besides, the reproducibility and stability of the LFIAs were tested on the same batch of test strips. Under optimal conditions, the sensitivity of LFIA was determined by testing different dilutions of the positive specimens. RESULTS: The proposed LFIAs were highly specific, and the limit of detection was as low as 25 ng/mL for SARS-CoV-2 antigens. The clinical applicability was evaluated with 659 samples (230 positive and 429 negative samples) by using both LFIA and rRT-PCR. Youden's index (J) was used to assess the performance of these diagnostic tests. The sensitivity and specificity were 98.22% and 97.93%, respectively, and J is 0.9615. The sensitivity and specificity were 98.22% and 97.93%, respectively, and J is 0.9615. In addition, the consistency of our proposed LFIA was analyzed using Cohen's kappa coefficient (κ = 0.9620). CONCLUSION: We found disease stage, age, gender, and clinical manifestations have only a slight influence on the diagnosis. Therefore, the lateral flow immunoassay SARS-CoV-2 antigen test strip is suitable for point-of-care detection and provides a great application for SARS-CoV-2 epidemic control in the third-world countries.

Simple and Easy Synthesis of γ-Amido-dNTPs in Water and Their Polymerase Reaction Properties.

γ-Amido-modified 2'-deoxynucleoside triphosphates (dNTPs) and nucleoside triphosphates (NTPs) are becoming increasingly important as biological tools. We herein describe the simple and easy synthesis of γ-amido-dNTPs and -NTPs from commercially available corresponding dNTPs and NTPs in a one-pot reaction using water-soluble carbodiimide and ammonia solution. We examined the effects of synthesized γ-amido-dNTPs on the DNA polymerase reaction. The results obtained showed the incorporation of these derivatives into the DNA primer while maintaining nucleobase selectivity; however, their incorporation efficiency by DNA polymerase was lower than that of dNTP. This is the first study to demonstrate the successful synthesis of four sets of γ-amido-dNTPs and clarify their properties.

Versatile Functionalization of P25 Conjugated ND Nanocomposites for UV-Mediated Free Radical Scavenging and Facilitates Anti-Inflammation Potential in Human Cells.

In this work, we demonstrated that building different linking groups between nanodiamond (ND) and TiO2 (P25) could provide more effective protection under oxidative stress and ultraviolet (UV) light irradiation compared with the use of TiO2 alone. The establishment of ester (-C-O-O-R), amide (-CONH-), and epoxide-amine adduct (-NHCCO-) groups between ND-TiO2 composites was found to be critical in the generation of reactive oxygen species (ROS) by controlling their charge transfer behaviors. We hypothesized that linking groups between the composites dictate the performance of ROS generation from nano-TiO2 under UV-light irradiation due to the differences in linking groups. The results showed that hydroxyl radicals were attenuated by the incorporation of ND. An MTT cell proliferation assay was performed in human cells under the treatment of ND-TiO2 composites to investigate the impacts of composites on cell viability. The results from the luciferase reporter assay suggested they have anti-inflammatory activity and can reduce cellular DNA damage under ROS stimulation. A zebrafish model was also applied with the ND-TiO2 composite treatment to demonstrate the safety aspects of the composites in vivo and their biomedical application potential. Studies exploring ROS generation behaviors in different linking groups suggested that interactive functionalization between nanoparticles might be an ideal antioxidant and anti-inflammatory strategy.

Synthesis and characterization of chemically fueled supramolecular materials driven by carbodiimide-based fuels.

Many supramolecular materials in biological systems are driven to a nonequilibrium state by the irreversible consumption of high-energy molecules such as ATP or GTP. As a result, they exhibit unique dynamic properties such as a tunable lifetime, adaptivity or the ability to self-heal. In contrast, synthetic counterparts that exist in or close to equilibrium are controlled by thermodynamic parameters and therefore lack these dynamic properties. To mimic biological materials more closely, synthetic self-assembling systems have been developed that are driven out of equilibrium by chemical reactions. This protocol describes the synthesis and characterization of such an assembly, which is driven by carbodiimide fuels. Depending on the amount of chemical fuel added to the material, its lifetime can be tuned. In the first step, the protocol details the synthesis and purification of the peptide-based precursors for the fuel-driven assemblies by solid-phase peptide synthesis. Then, we explain how to analyze the kinetic response of the precursors to a carbodiimide-based chemical fuel by HPLC and kinetic models. Finally, we detail how to study the emerging assembly's macro- and microscopic properties by time-lapse photography, UV-visible spectroscopy, shear rheology, confocal laser scanning microscopy and electron microscopy. The procedure is described using the example of a colloid-forming precursor Fmoc-E-OH and a fiber-forming precursor Fmoc-AAD-OH to emphasize the differences in characterization depending on the type of assembly. The characterization of a precursor's transient assembly can be done within 5 d. The synthesis and purification of a peptide precursor requires 2 d of work.

Water-based carbodiimide mediated synthesis of polysaccharide-amino acid conjugates: Deprotection, charge and structural analysis.

We report here a one-step aqueous method for the synthesis of isolated and purified polysaccharide-amino acid conjugates. Two different types of amino acid esters: glycine methyl ester and L-tryptophan methyl ester, as model compounds for peptides, were conjugated to the polysaccharide carboxymethylcellulose (CMC) in water using carbodiimide at ambient conditions. Detailed and systematic pH-dependent charge titration and spectroscopy (infrared, nuclear magnetic resonance: 1H, 13C- DEPT 135, 1H- 13C HMBC/HSQC correlation), UV-vis, elemental and ninhydrin analysis provided solid and direct evidence for the successful conjugation of the amino acid esters to the CMC backbone via an amide bond. As the concentration of amino acid esters increased, a conjugation efficiency of 20-80% was achieved. Activated charcoal aided base-catalyzed deprotection of the methyl esters improved the solubility of the conjugates in water. The approach proposed in this work should have the potential to tailor the backbone of polysaccharides containing di- or tri-peptides.

A novel detergent-based decellularization combined with carbodiimide crosslinking for improving anti-calcification of bioprosthetic heart valve.

Currently, valve replacement surgery is the only therapy for the end-stage valvular diseases because of the inability of regeneration for diseased heart valves. Bioprosthetic heart valves (BHVs), which are mainly derived from glutaraldehyde (GA) crosslinked porcine aortic heart valves or bovine pericardium, have been widely used in the last decades. However, it is inevitable that calcification and deterioration may occur within 10-15 years, which are still the main challenges for the BHVs in clinic. In this study, N-Lauroylsarcosine sodium salt (SLS) combined with N-(3-Dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) were utilized to decellularize and crosslink the heart valves instead of GA treatment. The obtained BHVs exhibited excellent extracellular matrix stability and mechanical properties, which were similar with GA treatment. Moreover, the obtained BHVs exhibited betterin vitrobiocompatibilities than GA treatment. After subcutaneous implantation for 30 d, the obtained BHVs showed mitigated immune response and reduced calcification compare with GA treatment. Therefore, all the above results indicated that the treatment of SLS-based decellularization combined with EDC/NHS crosslink should be a promising method to fabricate BHVs which can be used in clinic in future.

Characterization and antibacterial properties of epsilon-poly- l-lysine grafted multi-functional cellulose beads.

In recent years, harmful microorganisms in water pose great harm to ecological environment and human health. To solve this problem, epsilon-poly-l-lysine (EPL) grafted cellulose beads were prepared via 2, 2, 6, 6-tetramethylpiperidine-1-oxyl (TEMPO) mediated oxidation and carbodiimide mediated cross-linking reaction. Hydroxyl groups on C6 of cellulose were oxidized to carboxyl groups by TEMPO and grafting reaction was achieved between newly formed carboxyl groups of cellulose and amino of EPL. The beads were characterized by FTIR, SEM, XRD and TGA. The crystalline form of cellulose transformed from cellulose I to cellulose II after being dissolved and regenerated. The grafted cellulose beads showed good antibacterial activities against Gram-negative Escherichia coli, Gram-positive Staphylococcus aureus and Alicyclobacillus acidoterrestris with 10 h. The beads could be biodegraded in soil after 28 days. It is expected that the bio-based composite beads could have potential applications in water purification and food treatment fields.

A Carbodiimide-Mediated P-C Bond-Forming Reaction: Mild Amidoalkylation of P-Nucleophiles by Boc-Aminals.

The first example of a carbodiimide-mediated P-C bond-forming reaction is described. The reaction involves activation of ß-carboxyethylphosphinic acids and subsequent reaction with Boc-aminals using acid-catalysis. Mechanistic experiments using 31P NMR spectroscopy and DFT calculations support the contribution of unusually reactive cyclic phosphinic/carboxylic mixed anhydrides in a reaction pathway involving ion-pair "swapping". The utility of this protocol is highlighted by the direct synthesis of Boc-protected phosphinic dipeptides, as precursors to potent Zn-aminopeptidase inhibitors.