Understanding the nanoparticle-protein corona complexes using computational and experimental methods

Nanoparticles (NP) have capability to adsorb proteins from biological fluids and form protein layer, which is called protein corona. As the cell sees corona coated NPs, the protein corona can dictate biological response to NPs. The composition of protein corona is varied by physicochemical properties of NPs including size, shape, surface chemistry. Processing of protein adsorption is dynamic phenomena; to that end, a protein may desorb or leave a surface vacancy that is rapidly filled by another protein and cause changes in the corona composition mainly by the Vroman effect. In this review, we discuss the interaction between NP and proteins and the available techniques for identification of NP-bound proteins. Also we review current developed computational methods for understanding the NP-protein complex interactions.

An investigation of hydrogen-bonding effects on the nitrogen and hydrogen electric field gradient and chemical shielding tensors in the 9-methyladenine real crystalline structure: a density functional theory study

Hydrogen-bonding effects in the real crystalline structure of 9-methyladenine, 9-MA, were studied using calculated electric field gradient, EFG, and chemical shielding, CS, tensors for nitrogen and hydrogen nuclei via density functional theory. The calculations were carried out at the B3LYP and B3PW91 levels with the 6-311++G basis set via the Gaussian 98 package. Nuclear quadrupole coupling constants, C(Q), and asymmetry parameters, eta(Q), are reported for (14)N and (2)H. The chemical shielding anisotropy, Deltasigma, and chemical shielding isotropy, sigma(iso), are also reported for (15)N and (1)H. The difference between the calculated parameters of the monomer and heptameric layer-like cluster 9-MA shows how much H-bonding interactions affect the EFG and CS tensors of each nucleus. This result indicates that N(10) (imino nitrogen) has a major role in H-bonding interactions, whereas that of N(9) is negligible. There is good agreement between the present calculated parameters and reported experimental data. Although some discrepancies were observed, this could be attributed to the different conditions which were applied for calculation and the experiments.

Density functional theory investigation of hydrogen bonding effects on the oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors of anhydrous chitosan crystalline structure

A systematic computational investigation was carried out to characterize the 17O, 14N and 2H electric field gradient, EFG, as well as 17O, 15N, 13C and 1H chemical shielding tensors in the anhydrous chitosan crystalline structure. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the target molecule in the crystalline phase were considered through a hexameric cluster. The computations were performed with the B3LYP method and 6-311++G(d,p) and 6-31++G(d,p) standard basis sets using the Gaussian 98 suite of programs. Calculated EFG and chemical shielding tensors were used to evaluate the 17O, 14N and 2H nuclear quadrupole resonance, NQR, and 17O, 15N, 13C and 1H nuclear magnetic resonance, NMR, parameters in the hexameric cluster, which are in good agreement with the available experimental data. The difference between the calculated NQR and NMR parameters of the monomer and hexamer cluster shows how much hydrogen bonding interactions affect the EFG and chemical shielding tensors of each nucleus. These results indicate that both O(3)-H(33)...O(5-3) and N-H(22)...O(6-4) hydrogen bonding have a major influence on NQR and NMR parameters. Also, the quantum chemical calculations indicate that the intra- and intermolecular hydrogen bonding interactions play an essential role in determining the relative orientation of EFG and chemical shielding principal components in the molecular frame axes.

DFT studies of acrolein molecule adsorption on pristine and Al-doped graphenes

The ability of pristine graphene (PG) and Al-doped graphene (AlG) to detect toxic acrolein (C3H4O) was investigated by using density functional calculations. It was found that C3H4O molecule can be adsorbed on the PG and AlG with adsorption energies about -50.43 and - v30.92 kcal mol(-1) corresponding to the most stable configurations, respectively. Despite the fact that interaction of C3H4O has no obvious effects on the of electronic properties of PG, the interaction between C3H4O and AlG can induce significant changes in the HOMO/LUMO energy gap of the sheet, altering its electrical conductivity which is beneficial to sensor designing. Thus, the AlG may be sensitive in the presence of C3H4O molecule and might be used in its sensor devices. Also, applying an external electric filed in an appropriate orientation (almost stronger than 0.01 a.u.) can energetically facilitate the adsorption of C3H4O molecule on the AlG.

A Study on the Intermolecular Hydrogen Bonds of α-Glycylglycine in Its Actual Crystalline Phase Using ab Initio Calculated 14N and 2H Nuclear Quadrupole Coupling Constants

alpha-Glycylglycine in its actual crystalline phase is studied by ab initio calculated nuclear quadrupole coupling constants. These physical quantities are computed for 2H and 14N in the hydrogen bonds. The type of hydrogen bond is the N-H...O type. The computations are performed with the RHF and B3LYP methods and 6-31++G** and 6-311++G** basis sets using the Gaussian 98 program. Values of the calculated nuclear quadrupole coupling constants are shown in Tables 1-3. The aim of this work is the study of 2H and 14N quadrupole coupling constants which contribute in the CON2H...O=CN2H type of hydrogen bond. The computed nuclear quadrupole coupling constants of 2H nuclei meet the related experimental values. In addition, the computed chi value of 14N belonging to the -CO-14NH- group agrees well with values obtained experimentally. However, there are some discrepancies between calculated 14N chi values of the N+H3 residue and experiments. Also, the values of these physical parameters are calculated for >C2H2 of alpha-glycylglycine in its crystalline phase. Calculations for these parameters are carried out in a single molecule using X-ray diffraction coordinates, too.

Influence of C-Doping on the B-11 and N-14 Quadrupole Coupling Constants in Boron-Nitride Nanotubes: A DFT Study

A computational study at the level of density functional theory (DFT) was carried out to investigate the influence of carbon doping (C-doping) on the 11B and 14N quadrupole coupling constants (CQ) in the (6,0) single-walled boron-nitride nanotube (BNNT). To this aim, a 10 Å length of BNNT consisting of 24 B atoms and 24 N atoms was selected where the end atoms are capped by hydrogen atoms. To follow the purpose, six C atoms were doped instead of three B and three N atoms as a central ring in the surface of the C-doped BNNT. The calculated CQ values for both optimized BNNT systems, raw and C-doped, reveal different electrostatic environments in the mentioned systems. It was also demonstrated that the end nuclei have the largest CQ values in both considered BNNT systems.

Influence of N–H…O and O–H…O hydrogen bonds on the 17O, 15N and 13C chemical shielding tensors in crystalline acetaminophen: A density functional theory study

A computational investigation was carried out to characterize the (17)O, (15)N and (13)C chemical shielding tensors in crystalline acetaminophen. We found that N-H...O and O-H...O hydrogen bonds around the acetaminophen molecule in the crystal lattice have different influences on the calculated (17)O, (15)N and (13)C chemical shielding eigenvalues and their orientations in the molecular frame of axes. The calculations were performed with the B3LYP method and 6-311++G(d, p) and 6-311+G(d) standard basis sets using the Gaussian 98 suite of programs. Calculated chemical shielding tensors were used to evaluate the (17)O, (15)N, and (13)C NMR chemical shift tensors in crystalline acetaminophen, which are in reasonable agreement with available experimental data. The difference between the calculated NMR parameters of the monomer and molecular clusters shows how much hydrogen-bonding interactions affect the chemical shielding tensors of each nucleus. The computed (17)O chemical shielding tensor on O(1), which is involved in two intermolecular hydrogen bonds, shows remarkable sensitivity toward the choice of the cluster model, whereas the (17)O chemical shielding tensor on O(2) involved in one N-H...O hydrogen bond, shows smaller improvement toward the hydrogen-bonding interactions. Also, a reasonably good agreement between the experimentally obtained solid-state (15)N and (13)C NMR chemical shifts and B3LYP/6-311++G(d, p) calculations is achievable only in molecular cluster model where a complete hydrogen-bonding network is considered. Moreover, at the B3LYP/6-311++G(d, p) level of theory, the calculated (17)O, (15)N and (13)C chemical shielding tensor orientations are able to reproduce the experimental values to a reasonably good degree of accuracy.

Investigation of C–H…OC and N–H…OC hydrogen-bonding interactions in crystalline thymine by DFT calculations of O-17, N-14 and H-2 NQR parameters

A computational study at the level of density functional theory (DFT) was carried out to investigate C-H...O=C and N-H...O=C hydrogen-bonding interactions (HBs) in the real crystalline cluster of thymine by O-17, N-14 and H-2 calculated nuclear quadrupole resonance (NQR) parameters. To perform the calculations, a hydrogen-bonded pentameric cluster of thymine was created using X-ray coordinates where the hydrogen atoms positions are optimized and the electric field gradient (EFG) tensors were calculated for the target molecule. Additional EFG calculations were also performed for crystalline monomer and an optimized isolated gas-phase thymine. The calculated EFG tensors at the level of B3LYP and B3PW91 DFT methods and 6-311++G**and CC-pVTZ basis sets were converted to those experimentally measurable NQR parameters, quadrupole coupling constants and asymmetry parameters. The results reveal that because of strong contribution to N-H...O=C HBs, NQR parameters of O2, N1 and N3 undergo significant changes from monomer to the target molecule in cluster. Furthermore, the NQR parameters of O2 also undergo some changes because of non-classical C-H...O=C HBs.

Density functional calculations of oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors to study hydrogen bonding properties of peptide group (OC–NH) in crystalline acetamide

A density functional theory (DFT) study was carried out to investigate hydrogen bonding (HB) properties of peptide group (O=C-NH) in crystalline acetamide. Since the peptide group in acetamide contributes to N-H...O and C-H...O types of HB interactions, acetamide is considered as the simplest form of peptide linkage in proteins. The evaluated NMR parameters including quadrupole coupling constants and asymmetry parameters from the calculated electric field gradient (EFG) tensors at the sites of O17, N14 and H2 nuclei and isotropic chemical shieldings from the calculated chemical shielding (CS) tensors at the sites of O17, N15 and H1 nuclei reveal the major contribution of O=C-NH group to HB interactions. Although N-H...O type of HB interaction play the major role in the HB properties of peptide group in lattice form of crystalline acetamide, however, the role of weaker C-H...O type of HB interaction cannot be neglected.

A Systematic Investigation of Hydrogen-Bonding Effects on the 17O, 14N, and 2H Nuclear Quadrupole Resonance Parameters of Anhydrous and Monohydrated Cytosine Crystalline Structures: A Density Functional Theory Study

A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.

Theoretical investigation on the selective detection of SO2 molecule by AlN nanosheets

Theoretical calculations focused on the ability of an AlN nanosheet to detect O(3) and SO(2) molecules based on the dispersion corrected B3LYP (B3LYP-D) and B97D density functionals. Equilibrium geometries, stabilities, and the electronic properties of O(3) and SO(2) adsorptions on the surface of an AlN sheet were explored. The adsorption energies were calculated to be about -17.80 and -21.51 kcal mol(-1) at B3LYP-D level for O(3) and SO(2) corresponding to the most stable configurations, respectively. It was shown that the electrical conductance of the AlN sheet may be increased after the SO(2) adsorption, being somewhat insensitive to the O(3) adsorption. Thus, the AlN sheet may selectively detect SO(2) molecules in the presence of O(3) molecules.

A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α-glycine

A density functional theory (DFT) study was carried out to calculate (17)O, (14)N and (2)H electric field gradient (EFG) tensors in accurate neutron diffraction structures of alpha-glycine at 288 and 427 K. B3LYP is the used method and 6-311+G(*) and 6-311++G(**) are the basis sets in the calculations of EFG tensors at the sites of (17)O, (14)N and (2)H nuclei in the monomer and the octameric cluster of alpha-glycine at two temperatures. Quadrupole coupling constants and asymmetry parameters are the converted parameters of calculated EFG tensors to experimentally measurable ones. The calculated results of monomer and the target molecule in octameric cluster reveal that hydrogen-bonding interactions play an important role in the crystalline structure of alpha-glycine where the results of the target molecule in octameric cluster are in good agreement with the experiments.