Showing papers in "Journal of Theoretical and Computational Chemistry in 2014"

On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.

Abstract: Traditional implicit methods for modeling electrostatics in biomolecules use a two-dielectric approach: a biomolecule is assigned low dielectric constant while the water phase is considered as a high dielectric constant medium. However, such an approach treats the biomolecule-water interface as a sharp dielectric border between two homogeneous dielectric media and does not account for inhomogeneous dielectric properties of the macromolecule as well. Recently we reported a new development, a smooth Gaussian-based dielectric function which treats the entire system, the solute and the water phase, as inhomogeneous dielectric medium (J Chem Theory Comput. 2013 Apr 9; 9(4): 2126-2136.). Here we examine various aspects of the modeling of polar solvation energy in such inhomogeneous systems in terms of the solute-water boundary and the inhomogeneity of the solute in the absence of water surrounding. The smooth Gaussian-based dielectric function is implemented in the DelPhi finite-difference program, and therefore the sensitivity of the results with respect to the grid parameters is investigated, and it is shown that the calculated polar solvation energy is almost grid independent. Furthermore, the results are compared with the standard two-media model and it is demonstrated that on average, the standard method overestimates the magnitude of the polar solvation energy by a factor 2.5. Lastly, the possibility of the solute to have local dielectric constant larger than of a bulk water is investigated in a benchmarking test against experimentally determined set of pKa's and it is speculated that side chain rearrangements could result in local dielectric constant larger than 80.

Recent progress in adapting Poisson–Boltzmann methods to molecular simulations

Abstract: Electrostatic solvation modeling based upon the Poisson–Boltzmann equation is widely used in studies of biomolecular structures and functions. This manuscript provides a thorough review of published efforts to adapt the numerical Poisson–Boltzmann methods to molecular simulations so that these methods can be extended to biomolecular studies involving conformational fluctuation and/or dynamics. We first review the fundamental works on how to define the electrostatic free energy and the Maxwell stress tensor. These topics are followed by three different strategies in developing algorithms to compute electrostatic forces and how to improve their numerical performance. Finally procedures are also presented in detail on how to discretize these algorithms for numerical calculations. Given the pioneer works reviewed here, further developmental efforts will be on how to balance efficiency and accuracy in these theoretical sound approaches — two important issues in applying any numerical algorithms for routine biomolecular applications. Even if not reviewed here, more advanced numerical solvers are certainly necessary to achieve higher accuracy than the widely used classical methods to improve the overall performance of the numerical Poisson–Boltzmann methods.

Quantum-chemical study on relationship between structure and antioxidant properties of hepatoprotective compounds occurring in Cynara scolymus and Silybum marianum

Abstract: Accurate quantum computations based on the density functional theory have been performed to study the relationship between the electronic geometry and antioxidant capacity of chlorogenic acid, sily...

Accuracy of continuum electrostatic calculations based on three common dielectric boundary definitions.

Abstract: We investigate the influence of three common definitions of the solute/solvent dielectric boundary (DB) on the accuracy of the electrostatic solvation energy ΔGel computed within the Poisson Boltzmann and the generalized Born models of implicit solvation. The test structures include small molecules, peptides and small proteins; explicit solvent ΔGel are used as accuracy reference. For common atomic radii sets BONDI, PARSE (and ZAP9 for small molecules) the use of van der Waals (vdW) DB results, on average, in considerably larger errors in ΔGel than the molecular surface (MS) DB. The optimal probe radius ρw for which the MS DB yields the most accurate ΔGel varies considerably between structure types. The solvent accessible surface (SAS) DB becomes optimal at ρw ~ 0.2 A (exact value is sensitive to the structure and atomic radii), at which point the average accuracy of ΔGel is comparable to that of the MS-based boundary. The geometric equivalence of SAS to vdW surface based on the same atomic radii uniformly increased by ρw gives the corresponding optimal vdW DB. For small molecules, the optimal vdW DB based on BONDI + 0.2 A radii can yield ΔGel estimates at least as accurate as those based on the optimal MS DB. Also, in small molecules, pairwise charge-charge interactions computed with the optimal vdW DB are virtually equal to those computed with the MS DB, suggesting that in this case the two boundaries are practically equivalent by the electrostatic energy criteria. In structures other than small molecules, the optimal vdW and MS dielectric boundaries are not equivalent: the respective pairwise electrostatic interactions in the presence of solvent can differ by up to 5 kcal/mol for individual atomic pairs in small proteins, even when the total ΔGel are equal. For small proteins, the average decrease in pairwise electrostatic interactions resulting from the switch from optimal MS to optimal vdW DB definition can be mimicked within the MS DB definition by doubling of the solute dielectric constant. However, the use of the higher interior dielectric does not eliminate the large individual deviations between pairwise interactions computed within the two DB definitions. It is argued that while the MS based definition of the dielectric boundary is more physically correct in some types of practical calculations, the choice is not so clear in some other common scenarios.

Biological applications of classical electrostatics methods

Abstract: Continuum electrostatics modeling of solvation based on the Poisson–Boltzmann (PB) equation has gained wide acceptance in biomolecular applications such as energetic analysis and structural visualization. Successful application of the PB solvent models requires careful calibration of the solvation parameters. Extensive testing and validation is also important to ensure accuracy in their applications. Limitation in the continuum modeling of solvation is also a known issue in certain biomolecular applications. Growing interest in membrane systems has further spurred developmental efforts to allow inclusion of membrane in the PB solvent models. Despite their past successes due to careful parameterization, algorithm development and parallel implementation, there is still much to be done to improve their transferability from the small molecular systems upon which they were developed and validated to complex macromolecular systems as advances in technology continue to push forward, providing ever greater computational resources to researchers to study more interesting biological systems of higher complexity.

Assessing the performance of commonly used DFT functionals in studying the chemistry of frustrated Lewis pairs

Abstract: The benchmark study has assessed the performance of 18 density functional theory (DFT) functionals, including GGAs, hybrid-GGAs, meta-GGAs, and hybrid meta-GGAs, in predicting bonding strength, barrier height and structure for systems involving Lewis acids and bases. Three databases were built for the study, including 15 bonding enthalpies of dative bonds (DBH15), 10 reaction barriers (BH10) and 10 X-ray structures (XCS10). Wavefunction-based ab initio calculations were also carried out for comparisons. The benchmark data were computed at the CCSD(T)/BSI//MP2/BSI(BSI=aug-cc-pVTZ) level. The 6-311++G(d,p)(BSII) and 6-31G(d,p)(BSIII) basis sets were employed in DFT calculations. Generally, M06-2X/BSII and M05-2X/BSII outperform the other tested DFT methods. M05-2X/BSIII and M06-2X/BSIII are less accurate than M05-2X/BSII and M06-2X/BSII (or M05-2X/BSII//M05-2X/BSIII and M06-2X/BSII//M06-2X/BSIII), suggesting that large basis sets (e.g. BSII) are necessary to improve energetics. SCS-MP2 is less accurate than MP2, consistently overestimating bonding enthalpies and reaction barriers. Moreover, six DFT functionals (M05-2X, M06-2X, B3LYP, ωB97X-D, BMK and B97-D) were examined by comparing with the experimental bonding enthalpies of eighteen donor–acceptor complexes, which indicate that M05-2X and M06-2X are still better than others. Nevertheless, M05-2X and M06-2X significantly overestimate or underestimate the bonding enthalpies of F-substituted complexes, implying the necessity of improving the two functionals for describing fluorides. Using the six basis sets (BSI, cc-pVTZ, aug-cc-pVDZ, cc-pVDZ, TZVP and BSII) and DBH15 and BH10 databases, the influence of the basis sets on the performance of M06-2X functional was examined, which reveals that BSII is the most suitable basis set for the functional.

Study of dispersion of boron nitride nanotubes by triton X-100 surfactant using molecular dynamics simulations

Abstract: In this study, the dispersion of aggregated boron nitride nanotubes (BNNTs) in aqueous triton X-100 surfactant solution is studied using molecular dynamic simulation. The results indicate that how in the presence of the surfactant, a space between two BNNTs is created, which leads to the dispersion of the BNNTs. The radial distribution functions (RDFs) of the atoms of BNNTs and hydrophilic and hydrophobic segments of the surfactant respect to atoms of water molecules show that in the presence of the surfactant, a layer of water molecules is located in the neighborhood of the BNNTs and then hydrophobic and hydrophilic segments of the surfactant reside at more distances of the BNNTs. In the absence of the surfactant, the hydrogen bond between nitrogen atom of the BNNT and hydrogen atom of water molecules is established and the distance between water molecules and the BNNTs is decreased with increase of the surfactant concentration. The obtained results for the surfactant radius of gyration and the interfacial angle between two BNNTs reveal more information about the arrangement of the surfactants around the BNNTs in the presence and in the absence of water molecules.

Thermodynamically controlled Diels–Alder reaction of 12-N-methylcytisine: A DFT study

Abstract: A DFT study was performed for the Diels–Alder traction of 12-N-methylcytisine with a number of dienophiles (in boiling toluene under atmospheric pressure), namely, N-phenylmaleimide, maleic anhydride, 2,4-benzoquinone, tetracyanoethylene and methyl methacrylate. It was shown that 12-N-methylcytisine selectively reacts with these dienophiles, only the reaction with N-phenylmaleimide (NPM) resulting in the formation of thermodynamically stable adducts, which is consistent with experimental data. This selectivity of 12-N-methylcytisine is attributable to the difference between the properties of the listed dienophiles, which is confirmed by the relative reactivity indices calculated within the framework of the frontier molecular orbital (FMO) and hard and soft (Lewis) acids and bases (HSAB) theories, the thermodynamic and activation parameters of the forward and retro-Diels–Alder reactions. According to analysis of the theoretical results, NPM is characterized by high chemical potential, hardness close to that of 12-N-methylcytisine, and commensurable heights of the activation barriers for the forward and reverse Diels–Alder reactions and also forms stable [4+2] adducts.

Density functional theory study of transition metals doped B80 fullerene

Abstract: Density functional theory calculations have been carried out to investigate 3d, Pd and Pt transition metal (TM) atoms exohedrally and endohedrally doped B80 fullerene. We find that the most preferred doping site of the TM atom gradually moves from the outer surface (TM = Sc), to the inner surface (TM = Ti and V) and the center (TM = Cr, Mn, Fe and Zn), then to the outer surface (TM = Co, Ni, Cu, Pd, and Pt) again with the TM atom varying from Sc to Pt. From the formation energy calculations, we find that doping TM atom can further improve the stability of B80 fullerene. The magnetic moments of doped V, Cr, Mn, Fe, Co and Ni atoms are reduced from their free-atom values and other TM atoms are completely quenched. Charge transfer and hybridization between 4s and 3d states of TM and 2s and 2p states of B were observed. The energy gaps of TM@B80 are usually smaller than that of the pure B80. Endohedrally doped B80 fullerene with two Mn and two Fe atoms were also considered, respectively. It is found that the antiferromagnetic (AFM) state is more energetically favorable than the ferromagnetic (FM) state for Mn2- and Fe2@B80. The Mn and Fe atoms carry the residual magnetic moments of ~ 3 μB and 2 μB in the AFM states.

Molecular simulation of ibuprofen passing across POPC membrane

Abstract: Permeability assessment is an important procedure in the drug development process, and drug partitioning in membrane bilayer is related to permeability. To investigate the pH dependence on drug partitioning, the process of different ionization state of ibuprofen passing across POPC bilayer was studied using molecular dynamics simulation. The results show that both atomic charge scheme and ionization state of the drug affect the value and shape of energy profile when passing across the POPC bilayer. The neutral ibuprofen (ibuprofen under acidic condition) has a much lower energy barrier as compared with the anionic ibuprofen (ibuprofen under basic condition). Meantime, hydrogen bond analysis also certifies that it is easy for neutral ibuprofen to pass from bulk water to bilayer center. Our calculation suggests that the ionization state of ibuprofen may be changed between neutral and anionic state when passing across membrane: it may be ionized outside the membrane and neutralized inside the membrane.

Modified Poisson–Boltzmann equations for characterizing biomolecular solvation

Abstract: Methods for computing electrostatic interactions often account implicitly for the solvent, due to the much smaller number of degrees of freedom involved. In the Poisson–Boltzmann (PB) approach the electrostatic potential is obtained by solving the Poisson–Boltzmann equation (PBE), where the solvent region is modeled as a homogeneous medium with a high dielectric constant. PB however is not exempt of problems. It does not take into account for example the sizes of the ions in the atmosphere surrounding the solute, nor does it take into account the inhomogeneous dielectric response of water due to the presence of a highly charged surface. In this paper we review two major modifications of PB that circumvent these problems, namely the size-modified PB (SMPB) equation and the Dipolar Poisson–Boltzmann Langevin (DPBL) model. In SMPB, steric effects between ions are accounted for with a lattice gas model. In DPBL, the solvent region is no longer modeled as a homogeneous dielectric media but rather as an assembly of self-orienting interacting dipoles of variable density. This model results in a dielectric profile that transits smoothly from the solute to the solvent region as well as in a variable solvent density that depends on the charges of the solute. We show successful applications of the DPBL formalism to computing the solvation free energies of isolated ions in water. Further developments of more accurately modified PB models are discussed.

A density functional theory study of the hydration of calcium ions confined in the interlayer space of montmorillonites

Abstract: The structures of Ca2+ hydrates in the interlayer space of montmorillonites (MMT) were studied by periodic density functional theory (DFT) calculations under the GGA/PBE approximation. Affected by the internal surfaces, which are rich of negative charge, the Ca2+ hydration exhibits different behaviors from that in gas phase. The Ca2+ is located at the six-oxygen-ring (SOR) on the internal surface in dry MMT, while the incoming water molecules bind with the Ca2+, the O atoms on surface, and/or with each other. The water molecules have a tendency of forming a hydrogen bond (HB) network that connects the upper and lower surfaces. Attracted by surrounding water molecules, the Ca2+ gradually moves outward with increasing number of water molecules. Moreover, the hydration energy (EH) of Ca2+ is determined not only by the interaction between Ca2+ and H2O, but also by that among Ca2+, H2O and the surfaces. As a result, the EH has only small changes for additional incoming water molecules, in contrast to the great and monotonic decrease in gas phase.

On the electrostatic properties of homodimeric proteins.

Abstract: A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology9(2):e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily in an electrostatic funnel. It is demonstrated that the electrostatic dipole moment of the dimer is predominantly perpendicular to the axis connecting the centers of the mass of the monomers. In addition, the surface points with highest potential are located in the proximity of the interfacial plane of the homodimeric complexes. These findings indicate that frequent homodimerization provides specific electrostatic features needed for the function of proteins.

Tautomeric transformations and reactivity of isoindole and sila-indole: A computational study

Abstract: In this work, the tautomeric transformations and reactivity of isoindole and sila-isoindole molecules has been explored using the B3LYP/6-311G(d,p) level of theory in gas and solution phases. These calculations show that isoindole isomer has more stability rather than 1-h-isoindole. There is identical trend in silated species. The frontier molecular orbitals (FMO) and band gap energy calculations were performed at the B3LYP/6-311G(d,p) level in gas and various solvent. Solvent effects have been analyzed by using the self-consistent reaction field (SCRF) method based on polarizable continuum model (PCM) in chloroform, chlorobenzene, dichloromethane and tetrahydrofurane. Thermodynamic parameters calculated at room temperature have been analyzed. Also, electron affinities were computed. Local reactivity descriptors as Fukui functions local softness and electrophilicity indices analyses are performed to find out the reactive sites within molecule. Density functional theory (DFT) calculations were performed to compute nitrogen-14 nuclear quadrupole resonance (NQR) spectroscopy parameters.

Transition metal Mo-doped boron clusters: A computational investigation

Abstract: Geometries associated with relative stabilities and energy gaps of the Mo-doped boron clusters have been investigated systematically by using density functional theory. The critical size of Mo-encapsulated Bn structures emerges as n = 10, the evaluated relative stabilities in term of the calculated fragmentation energies reveal that the MoB6 has enhanced stabilities over their neighboring clusters. Furthermore, the calculated polarities of the MoBn reveal that the hypercoordinated planar MoB10 wheel is a weakened polar molecule and MoB11 ring is a nonpolar molecule, and aromatic properties are discussed. Additionally, the MoB10 cluster with smaller highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) gap is supposed to be stronger chemical activity and smaller chemical hardness. Moreover, the recorded natural populations show that the charges transfer from boron framework to Mo atom. It should be pointed out that the remarkable charge-transfer features of MoBn clusters are distinctly similar to those of transitional metal (TM)-doped Sin clusters; growth-pattern of the TMBn depends on the doped TM impurity.

First principle investigations to enhance the charge transfer properties by bridge elongation

Abstract: The ground-state geometries of 2-cyano-5-(4-(phenyl(4-vinylphenyl)amino)phenyl) penta-2,4-dienoic acid (TC4) derivatives have been optimized by using density functional theory (DFT) at B3LYP/6-31G** level of theory. The effect of bridge has been investigated on the electronic and charge transfer properties. The distortion between triphenylamine unit and acceptor moieties revealed there would be recombination barrier. The excitation energies have been computed by time dependent DFT at PCM-CAM-B3LYP/6-31G** and PCM-LC-BLYP/6-31G** level of theories. The absorption spectrum of TC4 computed at PCM-CAM-B3LYP/6-31G** level of theory is in good agreement with the experimental evidence while PCM-LC-BLYP/6-31G** level of theory underestimate it. The electron injection, electronic coupling constant and light harvesting efficiency (LHE) improved by elongating the bridge. The superior electron injection, electronic coupling constant, LHE, LUMO lying above the conduction band of TiO2 and HOMO below the redox couple compared to parent molecule revealed that new designed materials would be efficient photosensitizers.

First-principles study on electronic structure and optical properties of In-doped GaN

Abstract: The In-doped GaN is investigated by first-principles calculations of plane wave ultra-soft pseudo-potential method based on the density functional theory (DFT). The band structure, electronic structure, density of states and optical properties are investigated. The results indicate that the band-gap becomes narrower and the absorption edge of optical properties is red-shifted with the increase in In-doped concentration. Meanwhile, the visible region has strong absorption properties, and the significant absorption peaks are observed near 3.0 eV and 6.1 eV. The other peaks correspond to the wavelength of absorption spectra from the ultraviolet portion extending to the infrared portion, which almost covers the entire solar spectrum. The studied results show that In-doped GaN can be applied as solar cell and transparent conductivity material.

Quantum chemical and molecular dynamics studies of imidazoline derivatives as corrosion inhibitor and quantitative structure–activity relationship (QSAR) analysis using the support vector machine (SVM) method

Abstract: The inhibition performance of 10 imidazoline molecules with number of carbon from 15 to 21 of hydrocarbon straight-chain was studied by weight-loss method and theoretical approaches. The main purpose was to build a quantitative structure–activity relationship (QSAR) between the structural properties and the inhibition efficiencies, and then to predict efficiencies of new corrosion inhibitors. The quantum chemical calculation suggested that the active region of imidazoline molecules was located on the imidazoline ring and hydrophilic group, and active sites were concentrated on the nitrogen atoms of the molecules and carbon atoms of hydrophilic group. A model in accordance with the real experimental solution was built in the molecular dynamics, and the equilibrium configuration indicated that the imidazoline molecules were adsorbed on Fe(110) surface in parallel manner. Descriptors for QSAR model building were selected by principal component analysis (PCA) and the model was built by the support vector machine (SVM) approach, which shows good performance since the value of correlation coefficient (R) was 0.99 and the root mean square error (RMSE) was 0.94. Additionally, six new imidazoline molecules were theoretically designed and the inhibition efficiencies of three molecules were predicted to be more than 86% by the established QSAR model.

Theoretical study of the substituent effect on the hydrogen atom transfer mechanism of the irigenin derivatives antioxidant action

Abstract: In this paper, 21 substituents with various electron donating and electron withdrawing characters were placed in available positions of irigenin in order to study their effect on the O–H bond dissociation enthalpy (BDE) via DFT/B3LYP method. Results indicated the substituents in X3 and X4 positions have exerted stronger influence upon BDE values of irigenin derivatives when compared with same substituents in X1 and X2 positions. The results show that intramolecular hydrogen bond effects are able to considerably stabilize the parents and radicals. The natural bond orbital (NBO) analysis results also confirmed the intramolecular hydrogen bond stabilization. The formation of strong intramolecular hydrogen bonds in several radicals results in low BDEs. The 3-OH BDE values for substituents in X2 position have linear dependencies with Hammett constants (Fig. 2 and Eq. (2)). Found dependencies are suitably linear, that can be important for the synthesis of novel antioxidants based on irigenin.

Protein's native structure is dynamically stabilized by electronic polarization

Abstract: In this paper, molecular dynamics (MD) simulations were performed for a number of benchmark proteins using both the standard assisted model building with energy refinement (AMBER) charge and the dynamically adjusted polarized protein-specific charge (DPPC) from quantum fragment calculations to provide accurate electrostatic interactions. Our result shows that proteins' dynamic structures drifted away from the native structures in simulations under standard (nonpolarizable) AMBER force field. For comparison, proteins' native structures were dynamically stable after a long time simulation under DPPC. The free energy landscape reveals that the native structure is the lowest energy conformation under DPPC, while it is not under standard AMBER charge. To further investigate the polarization effect on the stability of native structures of proteins, we restarted from some decoy structures generated from simulations using standard AMBER charges and then carried out further MD simulation using DPPC to refine those structures. Our study shows that the native structures from these decoy structures can be mostly recovered using DPPC and that the dynamic structures with the highest population in cluster analysis are in close agreement with the corresponding native structures. The current study demonstrates the importance of electronic polarization of protein in stabilizing the native structure.

Conformational space analysis of neutral and protonated glycine using a genetic algorithm for multi-modal search

Abstract: The genetic algorithm based on the Multi-Niche Crowding (MNC) method is used with the semi-empirical methods AM1 and PM3 in order to scan the potential energy surface (PES) of neutral and protonated glycine. The algorithm is implemented as a package of programs interfaced with MOPAC and piloted by scripts. Both methods AM1 and PM3 located six minima on the PES of neutral glycine and seven on the protonated glycine one, of which three are those of the N-protonated form and four of the O-protonated one.

Structural heterogeneity among four subunits in pyranose 2-oxidase: A molecular dynamics simulation study

Abstract: The homotetramer pyranose 2-oxidase (P2O) from Tetrametes multicolor contains flavin adenine dinucleotide (FAD) as a cofactor, and displays two conformers with different transient fluorescence spectra and lifetimes (ca. 0.1 ps and 360 ps). The ultrashort lifetimes of isoalloxazine (Iso) are ascribed to the photoinduced electron transfer (ET) from Trp168 to the excited Iso. Here, the structural heterogeneity among the four subunits in solution was studied by means of molecular dynamics simulation (MDS). The ET donor–acceptor distances in crystal and solution were compared. The distribution of the H-bond distances between Iso and the surrounding amino acids revealed appreciable differences among the four subunits. The structural fluctuations in two distant places were examined for the Iso-P and Iso-Q distances (where P and Q are Trp or Tyr) with the correlation coefficients between Iso-P and Iso-Q distances, revealing cooperative motions even though P and Q were more than 1 nm apart and located in different subunits. Moreover, distributions of the distances between Iso and its closest ionic amino acids markedly differed among the four subunits. Electrostatic (ES) energies between the Iso anion and the ionic amino acids in the entire protein were obtained using a static dielectric constant of 1. The ES energy in each subunit was strongly influenced by the other subunits, whilst the distributions of the ES energies greatly differed among the four subunits. This heterogeneous distribution of the ES energy between subunits may contribute to the large differences in the experimentally detected ET rates.

Theoretical study on phthalocynine-Fe(II)-based fluorescent sensors for cyanide anion

Abstract: Three fluorescent sensors bearing phthalocynine-Fe(II) moiety were designed specifically for detecting cyanide anions, and investigated by DFT/TDDFT method. Comparison of the geometrical and photophysical properties of these sensor molecules, equipped with H-, carbamoyl and phthalimino groups, provided a deep insight into the sensor–cyanide interactions. The binding energy calculation shows that all the three sensors have good selectivity to the cyanide anion. Especially, frontier molecular orbital analysis confirmed that there was a photoinduced electron transfer (PET) process in the sensor with phthalimino group upon the addition of cyanide anion. This process could cause the fluorescence change. As a result, the sensor with phthalimino group displayed several favorable sensing properties.

Free energy profiles of ion permeation and doxorubicin translocation in TolC

Abstract: The outer membrane protein TolC of Escherichia coli forms a channel-tunnel pore spanning the periplasmic space and outer membrane, serving as the main exit duct for bacteria multidrug resistance and protein export. Many aspects of the transport mechanism of TolC are still unclear. Here, we have investigated the substrate permeability and gating mechanism of TolC by calculating the potential of mean forces (PMFs) for transporting sodium ion and doxorubicin through TolC using the adaptive biasing force (ABF) method. The transport mechanism is turned out to be substrate dependent. It is found that the periplasmic gate is required to open for the passage of both Na+ and doxorubicin, but the conformational gating does not lead to permeation barrier for Na+ at this region. The extracellular loops and K283 residues cause permeation barriers for Na+ at the extracellular entrance, but not for doxorubicin due to the extensive interactions between the drug molecule and the protein. TolC exhibits high conformational flexibility during the transport of Na+, while doxorubicin seems to be able to stabilize TolC in the resting state with the periplasmic gate closed. The association of the TolC docking domain of AcrB does not lower the permeation barrier for doxorubicin at the periplasmic gate, while the gate opening induces the dissociation of the TolC–AcrB complex.

A computational study of hexachlorobenzene-soil organic matter-interactions

Abstract: The fate of hexachlorobenzene (HCB) in soil represents a critical environmental problem. Once HCB has reached the soil it will interact with soil constituents, especially soil organic matter (SOM). The understanding of this interaction is important for choosing effective remediation procedures. Here we report a study of binding of HCB to a test set of molecules, which was developed to mimic representative functional groups of SOM. The binding energy of complexes formed by HCB and the test set molecules were investigated at different levels of theory. Effects of different types of dispersion correction to DFT, basis sets and DFT-functionals have been studied. Moreover, the general ability of dispersion-corrected DFT to represent this interaction has been benchmarked against methods such as MP2 and CCSD. As a result the B3LYP-D3 dispersion correction combined with the 6-311++G(2d,2p) basis set was found to be a compromise between accuracy and efficiency and it is recommended for studying this type of non-covalent interaction. Moreover, the performance of the GROMOS force field in the description of this interaction has been tested.

First principles study on energetic, structural, and electronic properties of defective g-C3N4-zz3 nanotubes

Abstract: The energetic, electronic and structural properties of defective g-C3N4-zz3 nanotubes are considered based on spin-polarized density-functional theory calculations. Nine basic system types with vacancy defects are characterized by their stabilization energies and band gaps. It is found that the nitrogen atom denoted as N3 is the most favorable atom for a vacancy defect. In all cases, local bond reconstruction occurs in the presence of vacancy defects. The role of C/N bond rotations on the above properties has been also investigated. The results show that N1–C3 bond rotation is the most favorable rotational defect. In addition, the electronic properties of the semiconducting g-C3N4-zz3 nanotube with defects have been studied using band structure and density of states plots.

Third-order NLO property of beryllium-pyridyne complexes

Abstract: Six pyridyne isomers and their complexes with beryllium have been considered for the theoretical study of the third-order polarizability. The NLO properties are calculated by employing the DFT functionals BLYP, B3LYP, BHHLYP, B3PW91, BP86 and B2PLYP for the 6-311++G(d,p) basis set. The C-Be bond length in the complexes varies within 1.644 A–1.771 A indicating covalent interactions between the metal and pyridynes. The present investigation reveals that the magnitude of second-hyperpolarizability of pyridynes strongly enhances upon complex formation with beryllium. The maximum hyperpolarizability has been predicted for the 2,5-diberyllium pyridine complex. The lowest value of hyperpolarizability is obtained for the 2,3- and 3,4-diberyllium pyridine complexes. The chosen DFT methods predict almost identical pattern of variation of NLO property. The variation of second-hyperpolarizability has been satisfactorily explained by the excitation energy and transition dipole moment associated with the most dominant excited state.

DFT calculations of tin dioxide crystals containing heavily-doped fluorine

Abstract: First-principles calculations based on the density functional theory (DFT) within the generalized gradient approximation have been used in the present research. Fluorine doping in the SnO2 crystals has been carried out considering a number of different defect concentrations. Dopant influence upon structural, electronic and electrical properties of the tin dioxide has been discussed in detail. The system presents n-type electrical conductivity relating our work directly to a number of empirical studies in this area. An experimental fact that n-type conductivity tends to decrease at rather high fluorine impurity rates has been explained at the theoretical level.

DFT study on the interaction between atomic aluminum and graphene

Abstract: In the present work, molecular orbital calculations using cluster models were performed within density functional theory (DFT) in order to study the adsorption of an Al atom on regular and defective graphene. Depending on the theoretical treatment of electronic exchange and correlations effects, different bonding results for the adsorption on the perfect surface are obtained. On the other hand, they are very similar for Al adsorbed on a carbon monovacancy. On regular graphene, the adsorption is exothermic when the Perdew, Burke and Ernzerhof (PBE) functional is used and endothermic with the Becke, 3-parameter, Lee–Yang–Parr (B3LYP) functional. Regarding the defective graphene surface, it was shown that the carbon atoms of concave angles in the vacancy are the most reactive to a radical attack. The adsorption of an Al atom on the vacancy restores the trigonal symmetry lost after the extraction of the C atom from regular graphene. Complementary calculations performed at PBE level on both regular and defective surfaces imposing periodic conditions qualitatively support the results obtained with the cluster model.

Kinetic model for the large deformation of cylindrical gels

Abstract: Here we investigate the kinetic model for the large deformation theory of hydrogel under the outside stimulations. We present the large deformation dynamical model in the following two points. (1) The phase transition caused by the deformation gradient is concerned, which makes the model more integral. (2) Based on the steady-state model, the time-dependent large deformation model is proposed and the time developing process is investigated. Considering the force of the large deformation, we introduce the heat equation to express the transformation of the chemical potential. The extended model can be used to describe the development of the large deformation. We present numerical examples of the cylindrical hydrogel for one- and two-dimensional cases under pressure and stretch. Besides, some key parameters are studied to test the model.