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A hysteresis-free perovskite transistor with exceptional stability through molecular cross-linking and amine-based surface passivation

Kim HP, Vasilopoulou M, Ullah H, Bibi S, Ximim Gavim AE, Macedo AG, et al.

Nanoscale, 2020 Apr 14;12(14):7641-7650.
PMID: 32207472 DOI: 10.1039/c9nr10745b

Organo-metal halide perovskite field-effect transistors present serious challenges in terms of device stability and hysteresis in the current-voltage characteristics. Migration of ions located at grain boundaries and surface defects in the perovskite film are the main reasons for instability and hysteresis issues. Here, we introduce a perovskite grain molecular cross-linking approach combined with amine-based surface passivation to address these issues. Molecular cross-linking was achieved through hydrogen bond interactions between perovskite halogens and dangling bonds present at grain boundaries and a hydrophobic cross-linker, namely diethyl-(12-phosphonododecyl)phosphonate, added to the precursor solution. With our approach, we obtained smooth and compact perovskite layers composed of tightly bound grains hence significantly suppressing the generation and migration of ions. Moreover, we achieved efficient surface passivation of the perovskite films upon surface treatment with an amine-bearing polymer, namely polyethylenimine ethoxylated. With our synergistic grain and surface passivation approach, we were able to demonstrate the first perovskite transistor with a complete lack of hysteresis and unprecedented stability upon continuous operation under ambient conditions. Added to the merits are its ambipolar transport of opposite carriers with balanced hole and electron mobilities of 4.02 and 3.35 cm2 V-1 s-1, respectively, its high Ion/Ioff ratio >104 and the lowest sub-threshold swing of 267 mV dec-1 reported to date for any perovskite transistor. These remarkable achievements obtained through a cost-effective molecular cross-linking of grains combined with amine-based surface passivation of the perovskite films open a new era and pave the way for the practical application of perovskite transistors in low-cost electronic circuits.

Matched MeSH terms: Hydrogen Bonding
Self-assembly of a robust hydrogen-bonded octylphosphonate network on cesium lead bromide perovskite nanocrystals for light-emitting diodes

Brown AAM, Hooper TJN, Veldhuis SA, Chin XY, Bruno A, Vashishtha P, et al.

Nanoscale, 2019 Jul 07;11(25):12370-12380.
PMID: 31215940 DOI: 10.1039/c9nr02566a

We report the self-assembly of an extensive inter-ligand hydrogen-bonding network of octylphosphonates on the surface of cesium lead bromide nanocrystals (CsPbBr3 NCs). The post-synthetic addition of octylphosphonic acid to oleic acid/oleylamine-capped CsPbBr3 NCs promoted the attachment of octylphosphonate to the NC surface, while the remaining oleylammonium ligands maintained the high dispersability of the NCs in non-polar solvent. Through powerful 2D solid-state 31P-1H NMR, we demonstrated that an ethyl acetate/acetonitrile purification regime was crucial for initiating the self-assembly of extensive octylphosphonate chains. Octylphosphonate ligands were found to preferentially bind in a monodentate mode through P-O-, leaving polar P[double bond, length as m-dash]O and P-OH groups free to form inter-ligand hydrogen bonds. The octylphosphonate ligand network strongly passivated the nanocrystal surface, yielding a fully-purified CsPbBr3 NC ink with PLQY of 62%, over 3 times higher than untreated NCs. We translated this to LED devices, achieving maximum external quantum efficiency and luminance of 7.74% and 1022 cd m-2 with OPA treatment, as opposed to 3.59% and 229 cd m-2 for untreated CsPbBr3 NCs. This represents one of the highest efficiency LEDs obtained for all-inorganic CsPbBr3 NCs, accomplished through simple, effective passivation and purification processes. The robust binding of octylphosphonates to the perovskite lattice, and specifically their ability to interlink through hydrogen bonding, offers a promising passivation approach which could potentially be beneficial across a breadth of halide perovskite optoelectronic applications.

Matched MeSH terms: Hydrogen Bonding
Fulltext In Silico Screening of Aptamers Configuration against Hepatitis B Surface Antigen

Sabri MZ, Abdul Hamid AA, Sayed Hitam SM, Abdul Rahim MZ

Adv Bioinformatics, 2019;2019:6912914.
PMID: 31346332 DOI: 10.1155/2019/6912914

Aptamer has been long studied as a substitute of antibodies for many purposes. However, due to the exceeded length of the aptamers obtained in vitro, difficulties arise in its manipulation during its molecular conjugation on the matrix surfaces. Current study focuses on computational improvement for aptamers screening of hepatitis B surface antigen (HBsAg) through optimization of the length sequences obtained from SELEX. Three original aptamers with affinity against HBsAg were truncated into five short hairpin structured aptamers and their affinity against HBsAg was thoroughly studied by molecular docking, molecular dynamics (MD) simulation, and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method. The result shows that truncated aptamers binding on HBsAg "a" determinant region are stabilized by the dynamic H-bond formation between the active binding residues and nucleotides. Amino acids residues with the highest hydrogen bonds hydrogen bond interactions with all five aptamers were determined as the active binding residues and further characterized. The computational prediction of complexes binding will include validations through experimental assays in future studies. Current study will improve the current in vitro aptamers by minimizing the aptamer length for its easy manipulation.

Matched MeSH terms: Hydrogen Bonding
Exploring the interaction between tyrphostin 9 and human serum albumin using biophysical and computational methods

Kandandapani S, Ridzwan NFW, Mohamad SB, Tayyab S

J Biomol Struct Dyn, 2020 Sep;38(14):4134-4142.
PMID: 31552810 DOI: 10.1080/07391102.2019.1673210

Tyrphostin 9 (Tyr 9) is a potent platelet-derived growth factor receptor (PDGFR) inhibitor, which induces apoptosis in various cancer cell types. The binding of Tyr 9 to the major transport protein, human serum albumin (HSA) was investigated using several spectroscopic techniques and molecular docking method. Fluorescence quenching titration results showed progressive decrease in the protein fluorescence with increasing drug concentrations. A decreasing trend of the Stern-Volmer constant, Ksv with increasing temperature characterized the drug-induced quenching as static quenching, thus pointed towards the formation of Tyr 9-HSA complex. The binding constant of Tyr 9-HSA interaction was found to lie within the range 3.48-1.69 × 105 M-1 at three different temperatures, i.e. 15 °C, 25 °C and 35 °C, respectively and suggested intermediate binding affinity between Tyr 9 and HSA. The drug-HSA complex seems to be stabilized by hydrophobic forces, van der Waals forces and hydrogen bonds, as suggested from the thermodynamic data as well as molecular docking results. The far-UV and the near-UV CD spectral results showed slight alteration in the secondary and tertiary structures, respectively, of the protein upon Tyr 9 binding. Interaction of Tyr 9 with HSA also produced microenvironmental perturbations around protein fluorophores, as evident from the three-dimensional fluorescence spectral results but increased protein's thermal stability. Both competitive drug binding results and molecular docking analysis suggested Sudlow's Site I of HSA as the preferred Tyr 9 binding site. Communicated by Ramaswamy H. Sarma.

Matched MeSH terms: Hydrogen Bonding
Landfill leachate wastewater treatment to facilitate resource recovery by a coagulation-flocculation process via hydrogen bond

Cheng SY, Show PL, Juan JC, Chang JS, Lau BF, Lai SH, et al.

Chemosphere, 2021 Jan;262:127829.
PMID: 32768754 DOI: 10.1016/j.chemosphere.2020.127829

Recent trend to recover value-added products from wastewater calls for more effective pre-treatment technology. Conventional landfill leachate treatment is often complex and thus causes negative environmental impacts and financial burden. In order to facilitate downstream processing of leachate wastewater for production of energy or value-added products, it is pertinent to maximize leachate treatment performance by using simple yet effective technology that removes pollutants with minimum chemical added into the wastewater that could potentially affect downstream processing. Hence, the optimization of coagulation-flocculation leachate treatment using multivariate approach is crucial. Central composite design was applied to optimize operating parameters viz. Alum dosage, pH and mixing speed. Quadratic model indicated that the optimum COD removal of 54% is achieved with low alum dosage, pH and mixing speed of 750 mgL-1, 8.5 and 100 rpm, respectively. Optimization result showed that natural pH of the mature landfill leachate sample is optimum for alum coagulation process. Hence, the cost of pH adjustment could be reduced for industrial application by adopting optimized parameters. The inherent mechanism of pollutant removal was elucidated by FTIR peaks at 3853 cm-1 which indicated that hydrogen bonds play a major role in leachate removal by forming well aggregated flocs. This is concordance with SEM image that the floc was well aggregated with the porous linkages and amorphous surface structure. The optimization of leachate treatment has been achieved by minimizing the usage of alum under optimized condition.

Matched MeSH terms: Hydrogen Bonding
Zwitterion composite chitosan-epichlorohydrin/zeolite for adsorption of methylene blue and reactive red 120 dyes

Jawad AH, Abdulhameed AS, Reghioua A, Yaseen ZM

Int J Biol Macromol, 2020 Nov 15;163:756-765.
PMID: 32634511 DOI: 10.1016/j.ijbiomac.2020.07.014

In this research, an attempt to develop zwitterion composite adsorbent is conducted by modifying chitosan (CHS) with a covalent cross-linker (epichlorohydrin, ECH) and an aluminosilicate mineral (zeolite, ZL). The zwitterion composite adsorbent of chitosan-epichlorohydrin/zeolite (CHS-ECH/ZL) is performed multifunctional tasks by removing two structurally different cationic (methylene blue dye, MB), and anionic (reactive red 120 dye, RR120) dyes from aqueous solutions. The surface property, crystallinity, morphology, functionality, and charge of the CHS-ECH/ZL are analyzed using BET, XRD, SEM, FTIR, and pHpzc, analyses, respectively. The influence of pertinent parameters namely CHS-ECH/ZL dosage (0.02-0.5 g), solution pH (4-10), temperature (303-323K), initial dye concentration (30-400 mg/L), and contact time (0-600 min) on the MB and RR120 removal are tested. The research findings revealed that the adsorption isotherm at equilibrium well explained in according to the Freundlich isotherm model, and the recorded adsorption capacities of CHS-ECH/ZL are 156.1 and 284.2 mg/g for MB and RR120 respectively at 30 °C. The mechanism of MB and RR120 adsorption onto the CHS-ECH/ZL indicates various types of interactions namely, electrostatic interaction, hydrogen bonding, and Yoshida H-bonding in addition to n-π interaction. Overall, this research introduces CHS-ECH/ZL composite as an eco-friendly zwitterion adsorbent with good applicability towards the two structurally different cationic and anionic dyes from aqueous environment.

Matched MeSH terms: Hydrogen Bonding
Molecular dynamics simulations suggest changes in electrostatic interactions as a potential mechanism through which serine phosphorylation inhibits DNA Polymerase β's activity

Homouz D, Joyce-Tan KH, Shahir Shamsir M, Moustafa IM, Idriss H

J Mol Graph Model, 2018 01;79:192.
PMID: 29223917 DOI: 10.1016/j.jmgm.2017.11.002

DNA polymerase β is a 39kDa enzyme that is a major component of Base Excision Repair in human cells. The enzyme comprises two major domains, a 31kDa domain responsible for the polymerase activity and an 8kDa domain, which bind ssDNA and has a deoxyribose phosphate (dRP) lyase activity. DNA polymerase β was shown to be phosphorylated in vitro with protein kinase C (PKC) at serines 44 and 55 (S44 and S55), resulting in loss of its polymerase enzymic activity, but not its ability to bind ssDNA. In this study, we investigate the potential phosphorylation-induced structural changes for DNA polymerase β using molecular dynamics. The simulations show drastic conformational changes of the polymerase structure as a result of S44 phosphorylation. Phosphorylation-induced conformational changes transform the closed (active) enzyme structure into an open one. Further analysis of the results points to a key hydrogen bond and newly formed salt bridges as potential drivers of these structural fluctuations. The changes observed with S44/55 and S55 phosphorylation were less dramatic than S44 and the integrity of the H-bond was not compromised. Thus the phosphorylation of S44 is likely the major contributor to structural fluctuations that lead to loss of enzymatic activity.

Matched MeSH terms: Hydrogen Bonding
Fulltext Synthesis, biological activity and molecular docking of new tricyclic series as α-glucosidase inhibitors

Abuelizz HA, Iwana NANI, Ahmad R, Anouar EH, Marzouk M, Al-Salahi R

BMC Chem, 2019 Dec;13(1):52.
PMID: 31384800 DOI: 10.1186/s13065-019-0560-4

Diabetes is an emerging metabolic disorder. α-Glucosidase inhibitors, such as acarbose, delay the hydrolysis of carbohydrates by interfering with the digestive enzymes. This action decreases the glucose absorption and the postprandial glucose level. We have synthesized 25 tricyclic 2-phenoxypyrido[3,2-e][1,2,4]triazolo[1,5-a]pyrimidin-5(4H)-ones hybrids and evaluated their α-glucosidase inhibitory activity. Compounds 6h and 6d have shown stronger activity than that of acarbose. Compound 6h exhibited the highest inhibition with an IC50 of 104.07 µM. Molecular modelling studies revealed that compound 6h inhibits α-glucosidase due to the formation of a stable ligand-α-glucosidase complex and extra hydrogen bond interactions, and directed in the binding site by Trp329.25 tricyclic 2-phenoxypyrido[3,2-e][1,2,4]triazolo[1,5-a]pyrimidin-5(4H)-ones hybrids have been synthesized and evaluated their α-glucosidase inhibitory activity. Compounds 6h have shown stronger activity than that of acarbose.

Matched MeSH terms: Hydrogen Bonding
Fulltext Processing and Characterisation of Banana Leaf Fibre Reinforced Thermoplastic Cassava Starch Composites

Jumaidin R, Diah NA, Ilyas RA, Alamjuri RH, Yusof FAM

Polymers (Basel), 2021 Apr 28;13(9).
PMID: 33924842 DOI: 10.3390/polym13091420

Increasing environmental concerns have led to greater attention to the development of biodegradable materials. The aim of this paper is to investigate the effect of banana leaf fibre (BLF) on the thermal and mechanical properties of thermoplastic cassava starch (TPCS). The biocomposites were prepared by incorporating 10 to 50 wt.% BLF into the TPCS matrix. The samples were characterised for their thermal and mechanical properties. The results showed that there were significant increments in the tensile and flexural properties of the materials, with the highest strength and modulus values obtained at 40 wt.% BLF content. Thermogravimetric analysis showed that the addition of BLF had increased the thermal stability of the material, indicated by higher-onset decomposition temperature and ash content. Morphological studies through scanning electron microscopy (SEM) exhibited a homogenous distribution of fibres and matrix with good adhesion, which is crucial in improving the mechanical properties of biocomposites. This was also attributed to the strong interaction of intermolecular hydrogen bonds between TPCS and fibre, proven by the FT-IR test that observed the presence of O-H bonding in the biocomposite.

Matched MeSH terms: Hydrogen Bonding
Probing n-Octyl α-d-Glycosides Using Deuterated Water in the Lyotropic Phase by Deuterium NMR

Wan Iskandar WFN, Salim M, Patrick M, Timimi BA, Zahid NI, Hashim R

J Phys Chem B, 2021 05 06;125(17):4393-4408.
PMID: 33885309 DOI: 10.1021/acs.jpcb.0c10629

The lyotropic phase behavior of four common and easily accessible glycosides, n-octyl α-d-glycosides, namely, α-Glc-OC8, α-Man-OC8, α-Gal-OC8, and α-Xyl-OC8, was investigated. The presence of normal hexagonal (HI), bicontinuous cubic (VI), and lamellar (Lα) phases in α-Glc-OC8 and α-Man-OC8 including their phase diagrams in water reported previously was verified by deuterium nuclear magnetic resonance (2H NMR), via monitoring the D2O spectra. Additionally, the partial binary phase diagrams and the liquid crystal structures formed by α-Gal-OC8 and α-Xyl-OC8 in D2O were constructed and confirmed using small- and wide-angle X-ray scattering and 2H NMR. The average number of bound water molecules (nb) per headgroup in the Lα phase was determined by the systematic measurement of the quadrupolar splitting of D2O over a wide range of molar ratio values (glycoside/D2O), especially at high glucoside composition. The number of bound water molecules bound to the headgroup was found to be around 1.5-2.0 for glucoside, mannoside, and galactoside, all of which possesses four OH groups. In the case of xyloside, which has only three OH groups, the bound water content is ∼2.0. Our findings confirmed that the bound water content of all n-octyl α-d-glycosides studied is lower compared to the number of possible hydrogen bonding sites possibly due to the fact that most of the OH groups are involved in intralayer interaction that holds the lipid assembly together.

Matched MeSH terms: Hydrogen Bonding
Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos

Oyewusi HA, Huyop F, Wahab RA

J Biomol Struct Dyn, 2020 Oct 23.
PMID: 33094694 DOI: 10.1080/07391102.2020.1835727

The high dependency and surplus use of agrochemical products have liberated enormous quantities of toxic halogenated pollutants into the environment and threaten the well-being of humankind. Herein, this study performed molecular docking, molecular dynamic (MD) simulations, molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis, to identify the order of which the enzyme degrades different substrates, haloacids, haloacetate and chlorpyrifos. The study discovered that the DehH2 favored the degradation of haloacids and haloacetates (-3.3 - 4.6 kcal/mol) and formed three hydrogen bonds with Asp125, Arg201 and Lys202. Despite the inconclusive molecular docking result, chlorpyrifos was consistently shown to be the least favored substrate of the DehH2 in MD simulations and MM-PBSA calculations. Results of MD simulations revealed the DehH2-haloacid- (RMSD 0.15 - 0.25 nm) and DehH2-haloacetates (RMSF 0.05 - 0.25 nm) were more stable, with the DehH2-L-2CP complex being the most stable while the least was the DehH2-chlorpyrifos (RMSD 0.295 nm; RMSF 0.05 - 0.59 nm). The Molecular Mechanics Poisson-Boltzmann Surface Area calculations showed the DehH2-L-2CP complex (-24.27 kcal/mol) having the lowest binding energy followed by DehH2-MCA (-22.78 kcal/mol), DehH2-D-2CP (-21.82 kcal/mol), DehH2-3CP (-21.11 kcal/mol), DehH2-2,2-DCP (-18.34 kcal/mol), DehH2-2,3-DCP (-8.34 kcal/mol), DehH2-TCA (-7.62 kcal/mol), while chlorpyrifos was unable to spontaneously bind to DehH2 (+127.16 kcal/mol). In a nutshell, the findings of this study offer valuable insights into the rational tailoring of the DehH2 for expanding its substrate specificity and catalytic activity in the near future.Communicated by Ramaswamy H. Sarma.

Matched MeSH terms: Hydrogen Bonding
Sub-structure-based screening and molecular docking studies of potential enteroviruses inhibitors

James SA, Yam WK

Comput Biol Chem, 2021 Jun;92:107499.
PMID: 33932782 DOI: 10.1016/j.compbiolchem.2021.107499

Rhinoviruses (RV), especially Human rhinovirus (HRVs) have been accepted as the most common cause for upper respiratory tract infections (URTIs). Pleconaril, a broad spectrum anti-rhinoviral compound, has been used as a drug of choice for URTIs for over a decade. Unfortunately, for various complications associated with this drug, it was rejected, and a replacement is highly desirable. In silico screening and prediction methods such as sub-structure search and molecular docking have been widely used to identify alternative compounds. In our study, we have utilised sub-structure search to narrow down our quest in finding relevant chemical compounds. Molecular docking studies were then used to study their binding interaction at the molecular level. Interestingly, we have identified 3 residues that is worth further investigation in upcoming molecular dynamics simulation systems of their contribution in stable interaction.

Matched MeSH terms: Hydrogen Bonding
Natural DENV-2 NS2B/NS3 protease inhibitors from Myristica cinnamomea King

Sivasothy Y, Liew SY, Othman MA, Abdul Wahab SM, Hariono M, Mohd Nawi MS, et al.

Trop Biomed, 2021 Jun 01;38(2):79-84.
PMID: 33973577 DOI: 10.47665/tb.38.2.044

The NS2B/NS3 protease is crucial for the pathogenesis of the DENV. Therefore, the inhibition of this protease is considered to be the key strategy for the development of new antiviral drugs. In the present study, malabaricones C (3) and E (4), acylphenols from the fruits of Myristica cinnamomea King, have been respectively identified as moderate (27.33 ± 5.45 μM) and potent (7.55 ± 1.64 μM) DENV-2 NS2B/NS3 protease inhibitors, thus making this the first report on the DENV-2 NS2B/NS3 protease inhibitory activity of acylphenols. Based on the molecular docking studies, compounds 3 and 4 both have π-π interactions with Tyr161. While compound 3 has hydrogen bonding interactions with Gly151, Gly153 and Tyr161, compound 4 however, forms hydrogen bonds with Ser135, Asp129, Phe130 and Ile86 instead. The results from the present study suggests that malabaricones C (3) and E (4) could be employed as lead compounds for the development of new dengue antivirals from natural origin.

Matched MeSH terms: Hydrogen Bonding
QSAR and Pharmacophore Mapping Studies on Benzothiazinimines to Relate their Structural Features with anti-HIV Activity

Geethaavacini G, Poh GP, Yan LY, Deepashini R, Shalini S, Harish R, et al.

Med Chem, 2018;14(7):733-740.
PMID: 29807521 DOI: 10.2174/1573406414666180529091618

BACKGROUND: The development of severe drug resistance caused by the extensive use of anti-HIV agents has resulted in a greatly extensive reduction in these drugs efficacy.
OBJECTIVES: To identify the important pharmacophoric features and correlate 3D chemical structure of benzothiazinimines with their anti-HIV potential using 2D, 3D-QSAR and pharmacophore modeling studies.
METHODS: QSAR and pharmacophore mapping studies have been used to relate structural features. 2D QSAR and 3D QSAR studies were performed using partial least square and k-nearest neighbor methodology, coupled with various feature selection methods, viz. stepwise, genetic algorithm, and simulated annealing, to derive QSAR models which were further validated for statistical significance.
RESULTS: The physicochemical descriptor XAHydrophilicArea and SsOHE-index, and alignmentindependent descriptor T_C_Cl_6 showed significant correlation with the anti-HIV activity of benzothiazinimines in 2D QSAR. 3D QSAR results showed the significant effect of electrostatic and steric field descriptors in the anti-HIV potential of benzothiazinimines. The generated pharmacophore hypothesis demonstrated the importance of aromaticity and hydrogen bond acceptors.
CONCLUSION: The significant models obtained in this study suggested that these techniques could be used as a guidance for designing new benzothiazinimines with enhanced anti-HIV potential.

Matched MeSH terms: Hydrogen Bonding
Fulltext Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

Maiangwa J, Mohamad Ali MS, Salleh AB, Rahman RNZRA, Normi YM, Mohd Shariff F, et al.

PeerJ, 2017;5:e3341.
PMID: 28533982 DOI: 10.7717/peerj.3341

The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity.

Matched MeSH terms: Hydrogen Bonding
Probing the interaction of 2,4-dichlorophenoxyacetic acid with human serum albumin as studied by experimental and computational approaches

Tayyab S, Francis JA, Kabir MZ, Ghani H, Mohamad SB

Spectrochim Acta A Mol Biomol Spectrosc, 2019 Jan 15;207:284-293.
PMID: 30267976 DOI: 10.1016/j.saa.2018.09.033

To characterize the binding of a widely used herbicide, 2,4-dichlorophenoxyacetic acid (2,4-D) to the major transporter in human circulation, human serum albumin (HSA), multi-spectroscopic approaches such as fluorescence, absorption and circular dichroism along with computational methods were employed. Analysis of the fluorescence and absorption spectroscopic data confirmed the 2,4-D-HSA complex formation. A static quenching mechanism was evident from the inverse temperature dependence of the KSV values. The complex was stabilized by a weak binding affinity (Ka = 5.08 × 103 M-1 at 298 K). Quantitative analysis of thermodynamic data revealed participation of hydrophobic and van der Waals interactions as well as hydrogen bonds in the binding process. Circular dichroism and three-dimensional fluorescence spectral results showed structural (secondary and tertiary) changes in HSA as well as microenvironmental perturbation around protein fluorophores (Trp and Tyr residues) upon 2,4-D binding. Addition of 2,4-D to HSA was found to improve protein's thermal stability. Competitive displacement results as well as computational analyses suggested preferred location of the 2,4-D binding site as Sudlow's site I (subdomain IIA) in HSA.

Matched MeSH terms: Hydrogen Bonding
Fulltext Effect of Lignin Modification on Properties of Kenaf Core Fiber Reinforced Poly(Butylene Succinate) Biocomposites

Ahmad Saffian H, Hyun-Joong K, Md Tahir P, Ibrahim NA, Lee SH, Lee CH

Materials (Basel), 2019 Dec 05;12(24).
PMID: 31817323 DOI: 10.3390/ma12244043

In this study, the effects of lignin modification on the properties of kenaf core fiber reinforced poly(butylene succinate) biocomposites were examined. A weight percent gain (WPG) value of 30.21% was recorded after the lignin were modified with maleic anhydride. Lower mechanical properties were observed for lignin composites because of incompatible bonding between the hydrophobic matrix and the hydrophilic lignin. Modified lignin (ML) was found to have a better interfacial bonding, since maleic anhydrides remove most of the hydrophilic hydrogen bonding (this was proven by a Fourier-transform infrared (FTIR) spectrometer-a reduction of broadband near 3400 cm-1, corresponding to the -OH stretching vibration of hydroxyl groups for the ML samples). On the other hand, ML was found to have a slightly lower glass transition temperature, Tg, since reactions with maleic anhydride destroy most of the intra- and inter-molecular hydrogen bonds, resulting in a softer structure at elevated temperatures. The addition of kraft lignin was found to increase the thermal stability of the PBS polymer composites, while modified kraft lignin showed higher thermal stability than pure kraft lignin and possessed delayed onset thermal degradation temperature.

Matched MeSH terms: Hydrogen Bonding
Mechanical and antibacterial properties of paper coated with chitosan

Sarani Zakaria, Chin HC, Wan Haslinda Wan Ahmad, Hatika Kaco, Soon Wei Chook, Chi HC

Sains Malaysiana, 2015;44:905-911.

Recent developments have found the viability of chitosan as a new alternative additive in the pulp and paper technology.
This study was carried out to investigate the effect of chitosan as a paper coating which were prepared by dissolution in
acetic acid solution. The mechanical properties of coated paper were improved significantly compared with non-coated
paper. The FT-IR spectra showed peak evolution at 1558 cm-1 for coated paper due to the existence of amine group. Since
FT-IR spectra for the coated paper was almost identical to the chitosan spectrum, it is assumed that there is an obvious
physical interaction rather than the chemical interaction. The SEM micrographs showed that some of the chitosan has
occupied the pores and some of them adhered only on the surface. This may be due to the chemical similarities between
cellulose and chitosan which enhanced the strength of fiber matrixes via hydrogen bonding. The antibacterial property
of coated paper showed that chitosan in dried form has no significant effect but effective when applied as wet solution.

Matched MeSH terms: Hydrogen Bonding
Fulltext In vitro and in silico studies of chalcone synthase variant 2 in Boesenbergia rotunda and its substrate specificity

Sanmugavelan R, Teoh TC, Roslan N, Mohamed Z

Turk J Biol, 2018;42(3):213-223.
PMID: 30814883 DOI: 10.3906/biy-1710-107

In this study, transformation of BrCHS var 2 into B. rotunda cell suspension culture, followed by chalcone synthase enzymatic assay and HPLC analysis was conducted to investigate whether the substrate specificity for BrCHS var 2 is either cinnamoyl-CoA or p-coumaroyl-CoA. The HPLC profile showed an increase in the amount of pinocembrin chalcone when cinnamoyl-CoA and malonyl-CoA were added but not p-coumaroyl-CoA. Molecular docking was performed to explore the binding of cinnamoyl-CoA and p-coumaroyl-CoA to BrCHS var 2 receptor and the docking results showed that cinnamoyl-CoA formed numerous hydrogen bonds and more negative docked energy than p-coumaroyl-CoA. Cinnamoyl-CoA showed good interactions with Cys 164 to initiate the subsequent formation of pinocembrin chalcone, whereas the hydroxyl group of p-coumaroyl-CoA formed an unfavorable interaction with Gln 161 that caused steric hindrance to subsequent formation of naringenin chalcone. Docked conformation analysis results also showed that malonyl-CoA formed hydrogen bonding with Cys 164, His 303, and Asn 336 residues in BrCHS var 2. The results show that cinnamoyl-CoA is the preferred substrate for BrCHS var 2.

Matched MeSH terms: Hydrogen Bonding
Molecular Dynamics Simulations of Glycyrrhizic Acid Aggregates as Drug-Carriers for Paclitaxel

Hussain M

Curr Drug Deliv, 2019;16(7):618-627.
PMID: 30868954 DOI: 10.2174/1567201816666190313155117

BACKGROUND: Glycyrrhizic acid (GA) is a glycoside that has shown considerable promise as a penetration enhancer and drug carrier to improve the absorption of poorly water-soluble drugs. The aggregation behavior of GA and its ability to form large micelles at higher solution concentrations are thought to contribute to these bioavailability enhancing properties. The oral absorption of Paclitaxel (PTX) for example, an anti-cancer agent which exhibits poor oral bioavailability, has been found to significantly increase in the presence of GA.
METHODS: In an attempt to visualize the aggregation behavior of GA and its subsequent association with PTX, 100 ns molecular dynamics simulation of a 5 mM aqueous solution of GA with 10 molecules of PTX was conducted using GROMACS and an all-atom forcefield.
RESULTS: Aggregation of GA molecules was found to occur quickly at this level of saturation leading to two stable aggregates of 13 and 17 GA molecules with an effective radius of 10.17 nm to 10.92 nm. These aggregates form not in isolation, but together with PTX molecule embedded within the structures, which reduces the number of interactions and hydrogen-bonding with water.
CONCLUSION: GA aggregation occurs around PTX molecules in solution, forming co-joined GA-PTX cluster units at a ratio of 3:1. These clusters remain stable for the remainder of the 100ns simulation and serve to isolate and protect PTX from the aqueous environment.

Matched MeSH terms: Hydrogen Bonding

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