26 research outputs found
Towards a circular economy: fabrication and characterization of biodegradable plates from sugarcane waste
Bagasse pulp is a promising material to produce biodegradable plates. Bagasse is the fibrous residue that remains after sugarcane stalks are crushed to extract their juice. It is a renewable resource and is widely available in many countries, making it an attractive alternative to traditional plastic plates. Recent research has shown that biodegradable plates made from Bagasse pulp have several advantages over traditional plastic plates. For example, they are more environmentally friendly because they are made from renewable resources and can be composted after use. Additionally, they are safer for human health because they do not contain harmful chemicals that can leach into food. The production process for Bagasse pulp plates is also relatively simple and cost-effective. Bagasse is first collected and then processed to remove impurities and extract the pulp. The pulp is then molded into the desired shape and dried to form a sturdy plate. Overall, biodegradable plates made from Bagasse pulp are a promising alternative to traditional plastic plates. They are environmentally friendly, safe for human health, and cost-effective to produce. As such, they have the potential to play an important role in reducing plastic waste and promoting sustainable practices. Over the years, the world was not paying strict attention to the impact of rapid growth in plastic use. As a result, uncontrollable volumes of plastic garbage have been released into the environment. Half of all plastic garbage generated worldwide is made up of packaging materials. The purpose of this article is to offer an alternative by creating bioplastic goods that can be produced in various shapes and sizes across various sectors, including food packaging, single-use tableware, and crafts. Products made from bagasse help address the issue of plastic pollution. To find the optimum option for creating bagasse-based biodegradable dinnerware in Egypt and throughout the world, researchers tested various scenarios. The findings show that bagasse pulp may replace plastics in biodegradable packaging. As a result of this value-added utilization of natural fibers, less waste and less of it ends up in landfills. The practical significance of this study is to help advance low-carbon economic solutions and to produce secure bioplastic materials that can replace Styrofoam in tableware and food packaging production
Coumarin and Its Derivatives
Coumarins are widely distributed in nature and can be found in a large number of naturally occurring and synthetic bioactive molecules. The unique and versatile oxygen-containing heterocyclic structure makes them a privileged scaffold in Medicinal Chemistry. Many coumarin derivatives have been extracted from natural sources, designed, synthetized, and evaluated on different pharmacological targets. In addition, coumarin-based ion receptors, fluorescent probes, and biological stains are growing quickly and have extensive applications to monitor timely enzyme activity, complex biological events, as well as accurate pharmacological and pharmacokinetic properties in living cells. The extraction, synthesis, and biological evaluation of coumarins have become extremely attractive and rapidly developing topics. A large number of research and review papers have compiled information on this important family of compounds in 2020. Research articles, reviews, communications, and concept papers focused on the multidisciplinary profile of coumarins, highlighting natural sources, most recent synthetic pathways, along with the main biological applications and theoretical studies, were the main focus of this book. The huge and growing range of applications of coumarins described in this book is a demonstration of the potential of this family of compounds in Organic Chemistry, Medicinal Chemistry, and different sciences related to the study of natural products. This book includes 23 articles: 17 original papers and six review papers
Molecular Photochemistry
There have been various comprehensive and stand-alone text books on the introduction to Molecular Photochemistry which provide crystal clear concepts on fundamental issues. This book entitled "Molecular Photochemistry - Various Aspects" presents various advanced topics that inherently utilizes those core concepts/techniques to various advanced fields of photochemistry and are generally not available. The purpose of publication of this book is actually an effort to bring many such important topics clubbed together. The goal of this book is to familiarize both research scholars and post graduate students with recent advancement in various fields related to Photochemistry. The book is broadly divided in five parts: the photochemistry I) in solution, II) of metal oxides, III) in biology, IV) the computational aspects and V) applications. Each part provides unique aspect of photochemistry. These exciting chapters clearly indicate that the future of photochemistry like in any other burgeoning field is more exciting than the past
Squaramide-Naphthalimide Conjugates as Potential Self-Assembled Materials and as DNA Binders
This thesis entitled ‘Squaramide-Naphthalimide Conjugates as Potential Self-Assembled
Materials and as DNA Binders’ is divided in 7 chapters. Chapter 1 presents an introduction to
DNA, its function and structure. Various DNA binders were introduced in this section,
specifically currently studied naphthalimides as DNA intercalators, with potential as possible
treatments for various types of cancers. The H-bonding ability of squaramide and its potential
as a DNA binder to the negatively charged sugar phosphate backbone was discussed. Bis-intercalators were also described in detail and their strong DNA bis-intercalating ability was
also discussed. The proposed target bis-intercalators were introduced, with multiple modes of
binding to DNA, where the naphthalimide moieties would bis-intercalate into DNA, while the
squaramide would bind to the negatively charged sugar phosphate backbone of DNA.
In Chapter 2, the design and synthesis of novel compounds are discussed. The syntheses of the
desired compounds, the challenges encountered during synthesis and the change in the design
of the desired compounds was also described. Each compound was characterised with room
temperature NMR and it was concluded that after VT-NMR studies were performed, which
clearly indicated self-assembly properties of these novel compounds.
Chapter 3 describes the self-assembly properties of the novel squaramide containing bis-naphthalimides, which will involve various techniques including VT-NMR, UV absorbance
time studies, extinction coefficient studies and Scanning Electron Microscopy.
Chapter 4 discusses the possible DNA binding ability of the novel synthesised compounds
using UV-Vis absorbance, fluorescence and Ethidium Bromide Assays.
Chapter 5 gives an overall conclusion of the entire work carried out in this research and also
provides a perspective with the ideas for future work.
Chapter 6 contains the general experimental procedures including the synthesis and detailed
characterisation of each of the synthesised compounds.
Chapter 7, the Appendix section contains all supporting information
Information-Directed Hybridization of Abiotic, Sequence-Defined Oligomers
The capacity for sequence-specific polymer strands to selectively assemble into intricate, folded structures and multimeric complexes relies upon the information borne by their residue sequences. Particularly suitable for the formation of multi-dimensional structures, nucleic acids have emerged as sophisticated nanoconstruction media where encoded sequences self-assemble in a designed manner through the gradual cooling of denatured and dissociated strands from raised temperatures. Unfortunately, the weakness of the hydrogen bonds holding the strands together affords nanoconstructs with thermal and mechanical instabilities. In contrast, molecular self-assembly employing dynamic covalent interactions has contributed to the improved mechanical and chemical stabilities of resultant structures. Nevertheless, compared with supramolecular chemistries, dynamic covalent interactions suffer from low dissociation rates, impeding rearrangement amongst the assembled components and often result in the kinetic trapping of non-equilibrium species. To overcome this limitation, molecular architectures are generally restricted to homo-functionalized constituents bearing few reactive sites or utilize harsh self-assembly conditions.
This dissertation examines the deliberate equilibrium shifting of dynamic covalent interactions to fabricate sequence-selective molecular architectures with high degrees of functionalization. First, we explored the use of a Lewis acidic catalyst, scandium triflate, Sc(OTf)3, to affect the equilibrium of imine formation, a well-characterized dynamic covalent interaction. Here, high concentrations of scandium triflate, dissociated oligomeric-strands encoded with amine- and aldehyde-pendant group species. Upon removal of excess scandium triflate with a liquid-liquid extraction, the equilibrium was shifted as to promote imine-formation between complementary strands. Subsequent annealing of the self-assembly solutions at 70°C, enabling rearrangement and error-correction of out-of-registry or non-complementary sequences, afforded the simultaneous formation of three distinct information-bearing ladder species and a mechanism for information storage and retrieval of data by abiotic polymers. The information-directed self-assembly of encoded molecular ladders was further developed by incorporating an orthogonal reaction into the oligomeric strands to mimic the information dense, sequence-selective hybridization of DNA. Thus, the base-4 information-directed assembly of molecular ladders and grids bearing covalent bond-based rungs was demonstrated from encoded precursor strands using dual concurrent, orthogonal dynamic covalent interactions (i.e., amine/aldehyde and boronic acid/catechol condensation reactions).
Additionally, the self-assembly of well-characterized ladder species employing the thermally-reversible Diels-Alder cycloaddition reaction was explored to establish a self-assembly mechanism requiring an external stimulus to alleviate or eliminate kinetic trapping. By utilizing furan-protected maleimide and furfurylamine residues, sequence-defined strands were synthesized simultaneously bearing both furan and maleimide species while precluding premature hybridization and self-assembled in an information-directed manner to form distinct ladder species using a temperature-mediated process.
Finally, given the large-scale efforts underway to develop rapid SARS-CoV-2 (Severe Acute Respiratory Syndrome - coronavirus – 2) diagnostic tests, the fundamental principles of sequence-selective hybridization were applied to transform blood-typing tests into SARS-CoV-2 serology tests using robust gel card agglutination reactions in combination with easily prepared antibody-peptide bioconjugates.PHDChemical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162941/1/sleguiz_1.pd
A Molecular Dynamics Investigation of the Interactions between DNA and Other Biological Molecules
We used molecular dynamics simulations to investigate interactions between DNA and three antineoplastic drugs from the anthracycline family, viz. daunomycin, doxorubicin and idarubicin. This encompassed three important aspects of DNA/drug interactions, viz. conformational perturbations, dynamics and energetics.
First, we investigated the structural perturbations caused by intercalation of the drugs into DNA. We found, using the software PyralleX which simulates X-ray diffraction patterns, that the DNA tends to change into an intermediary conformation between canonical forms. Daunomycin, among the three drugs, caused the greatest conformational shift in the DNA. Structural perturbations were shared with the base pairs adjacent to the intercalation sites.
Second, we studied the effects of groove-binding on the supercoiling behaviour of closed-circular DNA using the coarse-grained force field SIRAH. In the case without drugs, we saw an accelerating upward trend in the supercoiling rate with the salinity of the solution. However, with the drugs, supercoiling was found to retard in hypernatremic environments. Anthracyclines were found to form multilayer complex systems within themselves, which were capable of bridging across two segments of DNA and stabilising the DNA structure.
Third, we calculated the free energy changes associated with the intercalation of anthracyclines into DNA, using hybrid coarse-grained / all-atom models for simulation and the novel "extended-system adaptive biasing force" method for analysis. The free energy changes of intercalation of daunomycin and doxorubicin were calculated theoretically to be (-7.27 +/- 0.23) kcal/mol and (-8.61 +/- 0.33) kcal/mol respectively, which are in close agreement with previous experimental data. It was found that the calculated free energy change of idarubicin’s intercalation is (-7.75 +/- 0.17) kcal/mol, i.e. between those of the previous two drugs. This work has demonstrated a new way of evaluating free energy changes of interactions, which could help in speeding up time-consuming drug discovery processes
Multireference approaches for excited states of molecules
Understanding the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in chemistry, molecular physics, molecular biology, and materials science. A substantial impact is exerted by the fascinating progress in time-resolved spectroscopy, which leads to a strongly growing demand for theoretical methods to describe the characteristic features of excited states accurately. Whereas for electronic ground state problems of stable molecules the quantum chemical methodology is now so well developed that informed nonexperts can use it efficiently, the situation is entirely different concerning the investigation of excited states. This review is devoted to a specific class of approaches, usually denoted as multireference (MR) methods, the generality of which is needed for solving many spectroscopic or photodynamical problems. However, the understanding and proper application of these MR methods is often found to be difficult due to their complexity and their computational cost. The purpose of this review is to provide an overview of the most important facts about the different theoretical approaches available and to present by means of a collection of characteristic examples useful information, which can guide the reader in performing their own applications
Molecular Dynamics Study of Supercoiled DNA Minicircles Tightly Bent and Supercoiled DNA in Atomistic Resolution
Towards the complete understanding of the DNA response to superhelical stress, sequence dependence structural disruptions on the ~100 base pairs supercoiled DNA minicircles were examined through a series of atomistic MD simulations. The results showed the effects from some subtle structural characteristics of DNA on defect formation, including flexibility at base pair step level and anisotropy, whose dynamic information are available only from atomistic MD simulations. For longer supercoiled DNA minicircles (240-340 bp), the molecules adapt into their writhed conformations. Writhe can be calculated by a Gauss’ integral performed along the DNA central axis path. A new mathematical definition for the DNA central axis path was developed for the more exact writhe calculation. Finally, atomistic representation of supercoiled 336 base pairs minicircles was provided by fitting the DNA structure obtained by explicitly solvated MD simulations into the density maps from electron cryo-tomography. Structural data were analysed and provided a decent explanation for the mechanism of the sequence specific binding of the enzyme topoisomerase 1B onto the negatively supercoiled DNA
Non-covalent interactions in organotin(IV) derivatives of 5,7-ditertbutyl- and 5,7-diphenyl-1,2,4-triazolo[1,5-a]pyrimidine as recognition motifs in crystalline self- assembly and their in vitro antistaphylococcal activity
Non-covalent interactions are known to play a key role in biological compounds due to their
stabilization of the tertiary and quaternary structure of proteins [1]. Ligands similar to purine rings,
such as triazolo pyrimidine ones, are very versatile in their interactions with metals and can act as
model systems for natural bio-inorganic compounds [2]. A considerable series (twelve novel
compounds are reported) of 5,7-ditertbutyl-1,2,4-triazolo[1,5-a]pyrimidine (dbtp) and 5,7-diphenyl-
1,2,4-triazolo[1,5-a]pyrimidine (dptp) were synthesized and investigated by FT-IR and 119Sn
M\uf6ssbauer in the solid state and by 1H and 13C NMR spectroscopy, in solution [3]. The X-ray
crystal and molecular structures of Et2SnCl2(dbtp)2 and Ph2SnCl2(EtOH)2(dptp)2 were described, in
this latter pyrimidine molecules are not directly bound to the metal center but strictly H-bonded,
through N(3), to the -OH group of the ethanol moieties. The network of hydrogen bonding and
aromatic interactions involving pyrimidine and phenyl
rings in both complexes drives their self-assembly. Noncovalent
interactions involving aromatic rings are key
processes in both chemical and biological recognition,
contributing to overall complex stability and forming
recognition motifs. It is noteworthy that in
Ph2SnCl2(EtOH)2(dptp)2 \u3c0\u2013\u3c0 stacking interactions between
pairs of antiparallel triazolopyrimidine rings mimick basepair
interactions physiologically occurring in DNA (Fig.1).
M\uf6ssbauer spectra suggest for Et2SnCl2(dbtp)2 a
distorted octahedral structure, with C-Sn-C bond angles
lower than 180\ub0. The estimated angle for Et2SnCl2(dbtp)2
is virtually identical to that determined by X-ray diffraction. Ph2SnCl2(EtOH)2(dptp)2 is
characterized by an essentially linear C-Sn-C fragment according to the X-ray all-trans structure.
The compounds were screened for their in vitro antibacterial activity on a group of reference
staphylococcal strains susceptible or resistant to methicillin and against two reference Gramnegative
pathogens [4] . We tested the biological activity of all the specimen against a group of
staphylococcal reference strains (S. aureus ATCC 25923, S. aureus ATCC 29213, methicillin
resistant S. aureus 43866 and S. epidermidis RP62A) along with Gram-negative pathogens (P.
aeruginosa ATCC9027 and E. coli ATCC25922). Ph2SnCl2(EtOH)2(dptp)2 showed good
antibacterial activity with a MIC value of 5 \u3bcg mL-1 against S. aureus ATCC29213 and also
resulted active against methicillin resistant S. epidermidis RP62A