On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study.

The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel ß-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol-1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.

Fluorescence anisotropy cytosensing of folate receptor positive tumor cells using 3D polyurethane-GO-foams modified with folic acid: molecular dynamics and in vitro studies.

Integrated polyurethane (PU)-based foams modified with PEGylated graphene oxide and folic acid (PU@GO-PEG-FA) were developed with the goal of capturing and detecting tumor cells with precision. The detection of the modified PU@GO-PEG surface through FA against folate receptor-overexpressed tumor cells is the basis for tumor cell capture. Molecular dynamics (MD) simulations were applied to study the strength of FA interactions with the folate receptor. Based on the obtained results, the folate receptor has intense interactions with FA, which leads to the reduction in the FA interactions with PEG, and so decreases the fluorescence intensity of the biosensor. The synergistic interactions offer the FA-modified foams a high efficiency for capturing the tumor cell. Using a turn-off fluorescence technique based on the complicated interaction of FA-folate receptor generated by target recognition, the enhanced capture tumor cells could be directly read out at excitation-emission wavelengths of 380-450 nm. The working range is between 1×10 2 to 2×10 4 cells mL -1 with a detection limit of 25 cells mL -1 and good reproducibility with relative standard deviation of 2.35%. Overall, findings demonstrate that the fluorescence-based biosensor has a significant advantage for early tumor cell diagnosis.

A molecular dynamic study on the ability of phosphorene for designing new sensor for SARS-CoV-2 detection.

Due to the dramatic increase in the number of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), designing new selective and sensitive sensors for the detection of this virus is of importance. In this research, by employing full atomistic molecular dynamics (MD) simulations, the interactions of the receptor-binding domain (RBD) of the SARS-CoV-2 with phosphorene and graphene nanosheets were analyzed to investigate their sensing ability against this protein. Based on the obtained results, the RBD interactions with the surface of graphene and phosphorene nanosheets do not have important effects on the folding properties of the RBD but this protein has unique dynamical behavior against each nanostructure. In the presence of graphene and phosphorene, the RBD has lower stability because due to the strong interactions between RBD and these nanostructures. This protein spreads on the surface and has lower structural compaction, but in comparison with graphene, RBD shows greater stability on the surface of the phosphorene nanosheet. Moreover, RBD forms a more stable complex with phosphorene nanosheet in comparison with graphene due to greater electrostatic and van der Waals interactions. The calculated Gibbs binding energy for the RBD complexation process with phosphorene and graphene are -200.37 and -83.65 kcal mol-1, respectively confirming that phosphorene has higher affinity and sensitivity against this protein than graphene. Overall, the obtained results confirm that phosphorene can be a good candidate for designing new nanomaterials for selective detection of SARS-CoV-2.

Sensing Ability of Hybrid Cyclic Nanopeptides Based on Thiourea Cryptands for Different Ions, A Joint DFT-D3/MD Study.

Theoretical studies, including quantum chemistry (QM) calculations and 25 ns molecular dynamic (MD) simulations, were performed on two types of hybrid cyclic nanopeptides (HCNPs) that are constructed of tren-capped cryptand (HCNP1) and 1,3,5-triethylbenzene-capped cryptand (HCNP2) for selective complex formation with OAC-, NO3-, HSO4-, F-, Br-, and Cl- ions in the gas phase and DMSO. Obtained data by M05-2X, M05-2X-D3, B3LYP, and B3LYP-D3 functionals indicated that HCNPs form a stable complex with F- in comparison to other ions. DFT-D3 results and quantum theory of atoms in molecules (QTAIM) analysis indicated that dispersion and electrostatic interactions are the most important driving forces in HCNP-ion complex formation, respectively. Moreover, HOMO-LUMO analysis reveals that the reactivity of HCNP2, due to a lower band gap, is more than HCNP1. High sensing ability of the studied HCNPs for different ions was confirmed by Fermi level shifting of HNCPs to higher values during the complex formation. Finally, MD simulation results in DMSO are in good agreement with QM calculations and indicate that F- forms the most stable complexes with HCNPs because of stronger electrostatic interactions.

Theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer, molecular dynamics and quantum mechanics approach.

In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.

A combined molecular dynamic and quantum mechanic study of the solvent and guest molecule effect on the stability and length of heterocyclic peptide nanotubes.

Molecular dynamic simulations were performed to investigate the stability of heterocyclic peptide nanotubes composed of 1,4-disubstituted-1,2,3-triazol ε-amino acid. 45 ns MD simulations were conducted on the cyclic peptide nanotube (CPNT) and cyclic peptide dimer in methanol, chloroform, and water and revealed that these structures are more stable in nonpolar solvents. MM-PBSA and MM-GBSA calculations were employed to analyze the solvent effect on the stability and length of the CPNT. These calculations showed that CPNT in chloroform was more stable and longer as compared to other solvents. In addition, the effect of the guest molecule (ethanol) inside the dimer and CPNT was investigated. The obtained results confirmed that guest molecule(s) stabilized the dimer and CPNT in all solvents. Quantum chemistry calculations on the cyclic peptide dimer were performed at the M06-2X/6-31G(d) level in the gas phase and three solvents. The obtained results from the quantum chemistry study were in good agreement with the MD simulation results. DFT calculations showed that the guest molecule stabilized the dimer structure and electrostatically interacted with the cyclic peptide dimer. Finally, for investigation of the solvent effects on the hydrogen bonds of the cyclic peptide dimer, NBO and AIM analysis were performed.

Antimicrobial peptide interactions with bacterial cell membranes.

Antimicrobial peptides (AMPs) are potential alternatives for common antibiotics because of their greater activity and efficiency against a broad range of viruses, bacteria, fungi, and parasites. In this project, two antimicrobial peptides including magainin 2 and protegrin 1 with α-helix and ß-sheet secondary structures were selected to investigate their interactions with different lipid bilayers such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), POPC/POPG (7:3), POPC/POPS (7:3), POPG/POPE(1:3), and POPG/POPE(3:1). The obtained structures of the AMPs illustrated that protegrin 1 cannot maintain its secondary structure in the solution phase in contrast to magainin 2. The head groups of the lipid units play a key role in the stability of the lipid bilayers. The head parts of the lipid membranes by increasing the internal H-bond contribute to membrane compactness. The POPG and POPS units inside the POPC/POPG and POPC/POPS membranes increase the order of the POPC units. The cationic residues of the AMPs form remarkable electrostatic interactions with the negatively charged membrane surfaces, which play a key role in the stabilization process of the peptide secondary structures. The Arg residues of protegrin 1 and the Gly1, Lys4, Lys10, Lys11, Lys14, and Glu19 of the magainin 2 have the most important roles in the complexation process. The values of Gibbs binding energies (ΔG) indicate that the complexation process between AMPs and different bacterial membranes is favorable from the thermodynamic viewpoint and AMPs could form stable complexes with the lipid bilayers. As a result of ΔG values, protegrin 1 forms a more stable complex with POPG/POPE(3:1), while the α-helix has more affinity to the POPG/POPE(1:3) bacterial membranes. Therefore, it can be considered that ß-sheet and α-helix AMPs are more effective against gram-positive and gram-negative bacteria, respectively. The results of this study can provide useful details about the antimicrobial peptide interactions with the bacterial cell, which can be employed for designing new antimicrobial materials with greater efficiency.Communicated by Ramaswamy H. Sarma.

Quantum chemistry aspects of the solvent effects on 3,4-dimethyl-2,5-dihydrothiophen-1,1-dioxide pyrolysis reaction.

A theoretical density functional theory (DFT) study was employed to investigate solvent effects on a retro-cheletropic ene reaction. The use of a nonpolar solvent in this retro-ene reaction is desirable to improve the reaction rate. Interactions between 14 different solvents and the reaction mixtures (reactant and transition state) were considered using DFT solvation calculations. These results were used to determine the role of solvents on the rate constants. Theoretical calculations at the B3LYP/6-311++G(d,p) level revealed that in the presence of solvents with low polarity the reaction becomes faster, which is in accordance with experimental data. Transition state-solvent interactions were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations between electron densities in bond critical points of the C-S bond and interaction energy as well as vibrational frequencies at the transition state have been investigated.

Application of amino acid ionic liquids for increasing the stability of DNA in long term storage.

The structural stability of DNA is important because of its biological activity. DNAs due to their inherent chemical properties are not stable in an aqueous solution, therefore, a long period of storage of DNA at the ambient condition in bioscience is of importance. Ionic liquids (ILs) as interesting alternatives compared to organic solvents and water due to their considerable properties can be used as new agents to increase the stability of DNA for a long period of storage. In this article, molecular dynamics (MD) simulations and quantum chemistry calculations were applied to investigate the effects of amino acid ionic liquids ([BMIM][Ala], [BMIM][Gly], [BMIM][Val], [BMIM][Pro] and [BMIM][Leu]) on the dynamical behavior and the structural stability of calf thymus DNA. Based on the obtained MD results ILs enter into the solvation shell of the DNA and push away the water molecules from the DNA surface. Structural analysis shows that [BMIM]+ cations can occupy the DNA minor groove without disturbing the double-helical structure of DNA. ILs due to strong electrostatic and van der Waals (vdW) interactions with the DNA structure contribute to the stability of the double-helical structure. Quantum chemistry calculations indicate that the interactions between the [BMIM]+ cation and DNA structure has an electrostatic character. Moreover, this cation forms a more stable complex with the CGCG region of the DNA in comparison with AATT base pairs. Overall, the results of this study can provide new insight into the application of ILs for maintaining DNA stability during long-term storage.Communicated by Ramaswamy H. Sarma.

On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation.

Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibitor for this virus is of great medical and public health importance. With this goal in mind, we investigate the affinity of different sialic acid-based compounds (ligands) against the hemagglutinin-neuraminidase (HN) protein of the mumps virus, using a combination of molecular dynamics (MD) simulations and quantum chemistry calculations. Our MD simulation results indicate that the ligands form stable complexes with the HN protein through a combination of electrostatic, van der Waals (vdW), and hydrogen bond (H-bond) interactions, which the electrostatic interactions play a more important role in the complexation process. Based on the obtained results from the structural analysis Arg381, Arg291, and Arg49 play a key role in the binding site interactions with the different ligands, in comparison with other residues. There are some candidates such as Neu5Acα2-6Galß1-4GlcNAcß, Neu5Acα2-3Galß1-3GlcNacß1-3Galß1-4Glc, and Neu5Acα2-6Galß1-4GlcNAcß1-3Galß1-4Glc that form more stable complexes with the HN than the α2-3-Sialyllactose confirmed by the calculated Gibbs binding energies (-39.65, -46.93, and -36.49 kcal.mol-1, respectively). To investigate the relationship between the molecular properties of the selected compounds and their affinity to the HN receptor, density functional theory dispersion corrected (DFT-D3) calculations were employed. According to our DFT-D3 results, neutral sialic acid-based compounds have lower reactivity to the mumps virus than the negativity charge structures. Moreover, by increasing the electronic chemical potential (µ) the vdW and H-bond interactions between drugs and the HN protein increase. In other words, by elevating the electron tendency of the selected ligands their affinity to the mumps virus increases. Our quantum chemistry calculations reveal that in addition to the structural features the molecular properties of the drugs can play important roles in their affinity and reactivity against the virus. The results of this study can provide useful details to design new compounds or improve their properties against the mumps virus.

On the interactions of peptides with gold nanoparticles: effects of sequence and size.

Peptide-based self-assembly and synthesis techniques have emerged as a viable approach to designing active and stable inorganic nanostructures in aqueous media. In the present study, we use all-atom molecular dynamic (MD) simulations to study the interactions of ten short peptides (namely A3, AgBP1, AgBP2, AuBP1, AuBP2, GBP1, Midas2, Pd4, Z1, and Z2) with different gold nanoparticles (of different diameters ranging from 2 to 8 nm). Our MD simulation results imply that the gold nanoparticles have a remarkable effect on the stability and conformational properties of peptides. Moreover, the size of the gold nanoparticles and the type of peptide amino acid sequences play important roles in the stability of the peptide-AuNP complexes. Our results reveal that some amino acids such as Tyr, Phe, Met, Lys, Arg, and Gln have direct contact with the metal surface in comparison with Gly, Ala, Pro, Thr, and Val residues. The peptide adsorption on the surface of the gold nanoparticles is favorable from the energetic viewpoint, in which the van der Waals (vdW) interactions between the peptides and metal surface can be considered as one of the driving forces for the complexation process. The calculated Gibbs binding energies indicate that AuNPs have more sensitivity against the GBP1 peptide in the presence of different peptides. Overall, the results of this study can provide new insight into the peptide interaction with the gold nanoparticles from the molecular viewpoint, which can be important for designing new biomaterials based on the peptides and gold nanoparticles.Communicated by Ramaswamy H. Sarma.

Adsorption Process of Various Antimicrobial Peptides on Different Surfaces of Cellulose.

Current antimicrobial challenges in hospitals, pharmaceutical production units, and food packaging have motivated the development of antimicrobial agents, among them the antimicrobial compounds based on cellulose and peptides. Herein, we develop molecular dynamics (MD) models to dissect and characterize the adsorption process of antimicrobial peptides (AMPs) such as protegrin 1, magainin 2, and cyclic indolicidin on various surfaces of cellulose including [-1-10], [1-10], [-100], [100], [-110], and [110]. Our results suggest that the magainin 2 antimicrobial peptide loses most of its initial helix form, spreads on the cellulose surface, and makes the most rigid structure with [110] surface. The cyclic indolicidin peptide has the lowest affinity to adsorb on the cellulose surfaces, and the protegrin 1 peptide successfully adsorbs on all the proposed cellulose surfaces. Our MD simulations confirmed that cellulose can improve the corresponding peptides' structural stability and change their secondary structures during adsorption. The [-1-10] and [100] surfaces of cellulose show considerable affinity against the AMPs, exhibiting greater interactions with and adsorption to the peptides. Our data imply that the stronger adsorptions are caused by a set of H-bonds, van der Waals, and electrostatic interactions, where van der Waals interactions play a prominent role in the stability of the AMP-cellulose structures. Our energy analysis results suggest that glutamic acid and arginine amino acids have key roles in the stability of AMPs on cellulose surfaces due largely to stronger interactions with the cellulose surfaces as compared with other residues. Our results can provide useful insight at the molecular level that can help design better antimicrobial biomaterials based on cellulose.

Smartphone-assisted lab-in-a-tube device using gold nanocluster-based aptasensor for detection of MUC1-overexpressed tumor cells.

Developing smartphone technology for point-of-care diagnosis is one of the current favorable trends in the field of biosensors. In fact, using smartphones can provide better accessibility and facility for rapid diagnosis of diseases. On the other hand, the detection of circulating tumor cells (CTCs) is one of the recent methods for the early diagnosis of cancer. Here, a new smartphone-assisted lab-in-a-tube device is introduced for the detection of Mucin 1 (MUC1) overexpressed tumor-derived cell lines using gold nanoclusters (GNCs)-based aptasensor. Accordingly, commercial polyurethane (PU) foam was first coated with graphene oxide (GO) to increase its surface area (8.45-fold), and improve its wettability. The surface of the resulting three-dimensional PU-GO (3DPU-GO) platform was then modified by MUC1 aptamer-GNCs to provide the required sensitivity and specificity through a turn "on/off" detection system. The proposed biosensor was first optimized with a spectrophotometer method. Afterward, findings were evaluated based on the red color intensity of the lab-in-a-tube system; and indicated the high ability of the biosensor for detection of MUC1-overexpressed tumor cell lines in the range of 250-20,000 cells mL-1 with a limit of detection of 221 cells mL-1. In addition, the developed biosensor showed a decent selectivity against positive-control cell lines (MCF-7, and HT-29) in comparison to negative-control cell lines (HEK293, and L929). Notably, the results represented good accordance with reference methods including spectroscopy devices. Ultimately, the results of this work bring a new perspective to the field of point-of-care detection and can be considered in future biosensors.

Effects of Ionic Liquids on the Stabilization Process of Gold Nanoparticles.

Improving the stability of the gold nanoparticles (AuNPs) is an important challenge in nanoscience, given that the activity and ubiquitous application of the AuNPs in different fields depend largely on their stability in the solution phase. Ionic liquids (ILs) can be used as new alternatives in comparison to water and organic solvents due to their considerable properties to elevate the stability and resistance of the AuNPs against aggregation for a long period of storage. In this study, we employ molecular dynamics simulation and quantum chemistry calculations to investigate the effects of amino acid ILs ([BMIM][Gly], [BMIM][Leu], [BMIM][Pro], [BMIM][Val], and [BMIM][Ala]) on the stability and aggregation process of the AuNPs from the molecular viewpoint. Our results suggest that ILs can prevent AuNP aggregation. These ILs penetrate the solvation shell of the nanoparticles and by increasing the electrostatic repulsions on the surface of the AuNPs improve their stability against aggregation. Moreover, the [BMIM]+ cation is more effective on the stability of the AuNPs in comparison with the corresponding anions. The ring of the cation, due to the stronger interaction with the AuNPs compared to the side chain, contributes predominantly to the stability of the nanostructures. Our quantum chemistry calculations confirm that dispersion interactions between the cation and anions of the ILs and the surface of gold play a key role in the stability of the IL-AuNP complexes. [Leu]- anion has the strongest dispersion interactions with the metal surface and forms the most stable complex with the AuNPs. Overall, the results of this study offer new insights into the properties of amino acid ILs as effective agents to improve the stability of AuNPs for long-term storage.

Effect of Ethanol and Urea as Solvent Additives on PSS-PDADMA Polyelectrolyte Complexation.

The effect of urea and ethanol additives on aqueous solutions of poly(styrenesulfonate) (PSS), poly(diallyldimethylammonium) (PDADMA), and their complexation interactions are examined here via molecular dynamics simulations, interconnected laser Doppler velocimetry, and quartz crystal microbalance with dissipation. It is found that urea and ethanol have significant, yet opposite influences on PSS and PDADMA solvation and interactions. Notably, ethanol is systematically depleted from solvating the charge groups but condenses at the hydrophobic backbone of PSS. As a consequence of the poorer solvation environment for the ionic groups, ethanol significantly increases the extent of counterion condensation. On the other hand, urea readily solvates both polyelectrolytes and replaces water in solvation. For PSS, urea causes disruption of the hydrogen bonding of the PSS headgroup with water. In PSS-PDADMA complexation, these differences influence changes in the binding configurations relative to the case of pure water. Specifically, added ethanol leads to loosening of the complex caused by the enhancement of counterion condensation; added urea pushes polyelectrolyte chains further apart because of the formation of a persistent solvation shell. In total, we find that the effects of urea and ethanol rise from changes in the microscopic-level solvation environment and conformation resulting from solvating water being replaced by the additive. The differences cannot be explained purely via considering relative permittivity and continuum level electrostatic screening. Taken together, the findings could bear significance in tuning polyelectrolyte materials' mechanical and swelling characteristics via solution additives.

Mesoporous silica@chitosan@gold nanoparticles as "on/off" optical biosensor and pH-sensitive theranostic platform against cancer.

A cancer nanotheranostic system was fabricated based on mesoporous silica@chitosan@gold (MCM@CS@Au) nanosystem targeted by aptamer toward the MUC-1 positive tumor cells. Subsequently, curcumin as an efficient herbal anticancer drug was first encapsulated into chitosan-triphosphate nanoparticles and then the resulted nanoparticle was loaded into the nanosystem (MCM@CS@Au-Apt). The nanosystem successful fabrication was approved at each synthesis step through FTIR, XRD, BET, DLS, FE-SEM, HRTEM, and fluorescence spectroscopy. Besides, the interaction between aptamer and curcumin was evaluated using full atomistic molecular dynamics simulations. The mechanism of curcumin release was likewise investigated through different kinetic models. Afterwards, the potential of the designed nanosystem in targeted imaging, and drug delivery was evaluated using fluorescence microscopy and flow cytometry. It was found that the energy transfer between the base pairs in the hairpin of double strands of DNA aptamer acts as a quencher for MCM@CS@Au fluorescence culminating in an "on/off" optical biosensor. On the other hand, the presence of pH-sensitive chitosan nanoparticles creates smart nanosystem to deliver more curcumin into the desired cells. Indeed, when the aptamer specifically binds to the MUC-1 receptor, its double strands separate under the low pH condition, leading to the drug release and the recovery of the fluorescence ("On" state). Based on the toxicity results, this nanosystem had more toxicity toward the MUC-1-positive tumor cells than MUC-1-negative cells, representing its selective targeting. Therefore, this nanosystem could be introduced as a smart anticancer nanotheranostic system for tracing particular biomarkers (MUC-1), non-invasive fluorescence imaging, and targeted curcumin delivery.

A theoretical approach on the ability of functionalized gold nanoparticles for detection of Cd2.

Cadmium (Cd) as a toxic element that is widely present in water, soil, and air has important effects on human health, therefore proposing an accurate and selective method for detection of this element is of importance. In this article, by employing full atomistic molecular dynamics (MD) simulations and density functional theory dispersion corrected (DFT-D3) calculations, the effects of 6-mercaptonicotinic acid (MNA) and L-cysteine (CYS) on the stability of gold nanoparticles (AuNPs) and their sensitivity against Cd2+ were investigated. The obtained results indicate that pure AuNPs are not stable in water, while functionalized AuNPs with CYS and MNA groups have considerable stability without aggregation. In other words, the functional groups on the surface of AuNPs elevate their resistance against aggregation by an increase in the repulsive interactions between the gold nanoparticles. Moreover, functionalized AuNPs have considerable ability for selective detection of Cd2+ in the presence of different metal ions. Based on the MD simulation results, MNA-CYS-AuNPs (functionalized AuNPs with both functional groups) have the maximum sensitivity against Cd2+ in comparison with MNA-AuNPs and CYS-AuNPs due to the strong electrostatic interactions. DFT-D3 calculations reveal that the most probable interactions between the metal ions and functional groups are electrostatic, and Cd2+ can aggregate functionalized AuNPs due to strong electrostatic interactions with MNA and CYS groups. Moreover, charge transfer and donor-acceptor analyses show that molecular orbital interactions between the functional groups and Cd2+ can be considered as the driving force for AuNPs aggregation. A good agreement between the theoretical results and experimental data confirms the importance of the molecular modeling methods as a fast scientific protocol for designing new functionalized nanoparticles for application in different fields.

Experimental and Simulation Study of the Solvent Effects on the Intrinsic Properties of Spherical Lignin Nanoparticles.

Spherical lignin nanoparticles (LNPs) fabricated via nanoprecipitation of dissolved lignin are among the most attractive biomass-derived nanomaterials. Despite various studies exploring the methods to improve the uniformity of LNPs or seeking more application opportunities for LNPs, little attention has been given to the fundamental aspects of the solvent effects on the intrinsic properties of LNPs. In this study, we employed a variety of experimental techniques and molecular dynamics (MD) simulations to investigate the solvent effects on the intrinsic properties of LNPs. The LNPs were prepared from softwood Kraft lignin (SKL) using the binary solvents of aqueous acetone or aqueous tetrahydrofuran (THF) via nanoprecipitation. The internal morphology, porosity, and mechanical properties of the LNPs were analyzed with electron tomography (ET), small-angle X-ray scattering (SAXS), atomic force microscopy (AFM), and intermodulation AFM (ImAFM). We found that aqueous acetone resulted in smaller LNPs with higher uniformity compared to aqueous THF, mainly ascribing to stronger solvent-lignin interactions as suggested by MD simulation results and confirmed with aqueous 1,4-dioxane (DXN) and aqueous dimethyl sulfoxide (DMSO). More importantly, we report that both LNPs were compact particles with relatively homogeneous density distribution and very low porosity in the internal structure. The stiffness of the particles was independent of the size, and the Young's modulus was in the range of 0.3-4 GPa. Overall, the fundamental understandings of LNPs gained in this study are essential for the design of LNPs with optimal performance in applications.

Glucose derivatives substitution and cyclic peptide diameter effects on the stability of the self-assembled cyclic peptide nanotubes; a joint QM/MD study.

Dynamical behavior and the stability of eighteen nanostructures composed of cyclic peptide (CP) with the general structure of the cyclo(CO(CH2)n=4, 6, 10COCyst), in the gas phase, water and chloroform were investigated during 50ns molecular dynamic (MD) simulations. CP dimers and cyclic peptide nanotubes (CPNTs) are more stable in chloroform than water and this stability is reversely correlated with the ring size of the CP units. Also the effect of glucose derivatives substitution, d-glucose (S1) and N-methyl-d-glucamine (S2), on the stability and other physicochemical properties of the CP dimers and CPNTs were evaluated. These substitutions increase the inner-subunits hydrogen bonds (H-bond) which in turn increase the stability of these structures. Moreover, the S2 substitution in comparison to the S1 makes dimers and CPNTs more stable. Gibbs free energy analysis based on the MM-PBSA and MM-GBSA calculations confirmed that substitutions affect the stability of the studied nanostructures, considerably and an increase in the length of the CPNT units reduces their stability. Quantum chemistry calculations on the dimer structures using the density functional theory (DFT) and DFT-D3 methods were performed. Based on the DFT-D3 calculations, it was revealed that the dispersion interactions play a key role in the dimerization process. The ring size increment, elevates the dispersion interaction energy which is accordance with the MD results. H-bond formation between the CO and NH groups of the CP units inside the dimers have been analyzed by using the quantum theory of atoms in molecules and natural bond orbital description. Finally, through these analyses, the electrostatic interaction between the mentioned groups have been evaluated.