Carbon and its analogous nanomaterials are beneficial for toxic gas sensors since they are used to increase the electrochemically active surface region and improve the transmission of electrons. The present article addresses a detailed investigation on the potential of the monolayer PC3 compound as a possible sensor material for environmentally toxic nitrogen-containing gases (NCGs), namely NH3, NO, and NO2. The entire work is carried out under the frameworks of density functional theory, ab-initio molecular dynamics simulations, and non-equilibrium Green's function approaches. The monolayer-gas interactions are studied with the van der Waals dispersion correction. The stability of pristine monolayer PC3 is confirmed through dynamical, mechanical, and thermal analyses. The mobility and relaxation time of 2D PC3 sensor material with NCGs are obtained in the range of 101-104 cm2 V-1 s-1 and 101-103 fs for armchair and zigzag directions, respectively. Out of six possible adsorption sites for toxic gases on the PC3 surface, the most prominent site is identified with the highest adsorption energy for all the NCGs. Considering the most stable configuration site of the NCGs, we have obtained relevant electronic properties by utilizing the band unfolding technique. The considerable adsorption energies are obtained for NO and NO2 compared to NH3. Although physisorption is observed for all the NCGs on the PC3 surface, NO2 is found to convert into NO and O at 5.05 ps (at 300 K) under molecular dynamics simulation. The maximum charge transfer (0.31e) and work function (5.17 eV) are observed for the NO2 gas molecule in the series. Along with the considerable adsorption energies for NO and NO2 gas molecules, their shorter recovery time (0.071 s and 0.037 s, respectively) from the PC3 surface also identifies 2D PC3 as a promising sensor material for those environmentally toxic gases. The experimental viability and actual implications for PC3 monolayer as NCGs sensor material are also confirmed by examining the humidity effect and transport properties with modeled sensor devices. The transport properties (I-V characteristics) reflect the significant sensitivity of PC3 monolayer toward NO and NO2 molecules. These results certainly confirm PC3 monolayer as a promising sensor material for NO and NO2 NCG molecules.
- MeSH
- Adsorption MeSH
- Nitrogen MeSH
- Electrons MeSH
- Nanostructures * MeSH
- Gases * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Arsenic is one of the inorganic pollutants typically found in natural waters, and its toxic effects on the human body are currently of great concern. For this reason, the search for detoxifying agents that can be used in a so-called "chelation therapy" is of primary importance. However, to the aim of finding the thermodynamic behavior of efficient chelating agents, extensive speciation studies, capable of reproducing physiological conditions in terms of pH, temperature, and ionic strength, are in order. Here, we report on the acid-base properties of meso-2,3-dimercaptosuccinic acid (DMSA) at different temperatures (i.e., T = 288.15, 298.15, 310.15, and 318.15 K). In particular, its capability to interact with As(III) has been investigated by experimentally evaluating some crucial thermodynamic parameters (ΔH and TΔS), stability constants, and its speciation model. Additionally, in order to gather information on the microscopic coordination modalities of As(III) with the functional groups of DMSA and, at the same time, to better interpret the experimental results, a series of state-of-the-art ab initio molecular dynamics simulations have been performed. For the sake of completeness, the sequestering capabilities of DMSA-a simple dithiol ligand-toward As(III) are directly compared with those recently emerged from similar analyses reported on monothiol ligands.
- MeSH
- Arsenic chemistry isolation & purification MeSH
- Chelating Agents chemistry MeSH
- Hydrogen-Ion Concentration MeSH
- Succimer chemistry MeSH
- Humans MeSH
- Ligands MeSH
- Molecular Structure MeSH
- Molecular Dynamics Simulation MeSH
- Body Fluids chemistry MeSH
- Thermodynamics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon-donor hydrogen bonds, OH-π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.
- MeSH
- Amino Acids analysis MeSH
- Databases, Protein MeSH
- Crystallography, X-Ray MeSH
- Humans MeSH
- Molecular Conformation MeSH
- Models, Molecular MeSH
- Proteins chemistry MeSH
- Protein Structure, Secondary MeSH
- Water analysis MeSH
- Hydrogen Bonding MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreement with ab initio calculations obtained in the Gaussian03 program. Dihedral torsions of active groups of betulin were determined for both procedures, and related calculated structures were compared successfully. The selected force field was used for subsequent optimization of betulin in a water environment, and a conformational search was performed using quench molecular dynamics. The total energies of betulin and its interactions in water bulk were calculated, and the influence of water on betulin structure was investigated.
Skin penetration enhancers are compounds used to facilitate the transdermal delivery of drugs that are otherwise not sufficiently permeable. Through a synthetic route implementing two series of esters, we generated transdermal penetration enhancers by a multi-step reaction with substituted 6-aminohexanoic acid. We present the synthesis of all newly prepared compounds here with structural confirmation accomplished by (1)H NMR, (13)C NMR, IR and mass spectroscopy (MS). The lipophilicity (logk) of all compounds was determined via RP-HPLC and their hydrophobicity (logP/ClogP) was also calculated using two commercially available programs. Ab initio calculations of geometry and molecular dynamic simulations were employed to investigate the 3-dimensional structures of selected compounds. The transdermal penetration-enhancing activity of all the synthesized esters were examined in vitro and demonstrated higher enhancement ratios than oleic acid. Compounds 2e (C(10) ester chain) and 2f (C(11) ester chain) exhibited the highest enhancement ratios. It can be concluded that the series non-substituted at the C((2)) position by a ω-lactam ring showed significantly higher activity than those with azepan-2-one. None of the prepared compounds penetrated through the skin. All of the investigated agents demonstrated minimal anti-proliferative activity using the SK-N-MC neuroepithelioma cell line (IC(50)>6.25μM), suggesting these analogs would have a low cytotoxic profile when administered in vivo as chemical penetration enhancers. The correlation between the chemical structure of the studied compounds and their lipophilicity is discussed in regards to transdermal penetration-enhancing activity.
- MeSH
- Administration, Topical MeSH
- Hydrophobic and Hydrophilic Interactions MeSH
- Caproates chemical synthesis chemistry pharmacology MeSH
- Skin Absorption MeSH
- Skin drug effects MeSH
- Aminocaproic Acid chemical synthesis chemistry pharmacology MeSH
- Humans MeSH
- Cell Line, Tumor MeSH
- Swine MeSH
- Antineoplastic Agents chemical synthesis chemistry pharmacology MeSH
- Pyrrolidines chemical synthesis chemistry pharmacology MeSH
- Molecular Dynamics Simulation MeSH
- Stereoisomerism MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
In this study, affinity capillary electrophoresis (ACE) and quantum mechanical density functional theory (DFT) calculations were combined to investigate non-covalent binding interactions between the hexaarylbenzene-based receptor (R) and alkali metal ions, Rb(+) and Cs(+) , in methanol. The apparent binding (stability) constants (K(b) ) of the complexes of receptor R with alkali metal ions in the methanolic medium were determined by ACE from the dependence of effective electrophoretic mobility of the receptor R on the concentration of Rb(+) and Cs(+) ions in the BGE using a non-linear regression analysis. The receptor R formed relatively strong complexes both with rubidium (log K(b) =4.04±0.21) and cesium ions (log K(b) =3.72±0.22). The structural characteristics of the above alkali metal ion complexes with the receptor R were described by ab initio density functional theory calculations. These calculations have shown that the studied cations bind to the receptor R because they synergistically interact with the polar ethereal fence and with the central benzene ring via cation-π interaction.
Skin penetration enhancers are used in the formulation of transdermal delivery systems for drugs that are otherwise not sufficiently skin-permeable. We generated two series of esters by multi-step synthesis with substituted 6-aminohexanoic acid as potential transdermal penetration enhancers by multi-step synthesis. The synthesis of all newly prepared compounds is presented here. Structure confirmation of all generated compounds was accomplished by (1)H NMR, (13)C NMR, IR and MS spectroscopy. All the prepared compounds were analyzed using RP-HPLC and their lipophilicity (logk) was determined. The hydrophobicity (logP/ClogP) of the studied compounds was also calculated using two commercially available programs and 3D structures of the selected compounds were investigated by means of ab initio calculations of geometry and molecular dynamic simulations. All the synthesized esters were tested for their in vitro transdermal penetration-enhancing activity and showed higher enhancement ratios than oleic acid. The highest enhancement ratios were exhibited by compound 5f (C((2)) substituted with piperidine-2-one, C(11) ester chain) and 5a (C((2)) substituted with piperidine-2-one, C(6) ester chain). The series with a ω-lactam ring (piperidin-2-one; 5a-g), showed slightly higher activities than those with morpholine (6a-6g). All of the agents showed minimal anti-proliferative activity (IC(50) >6.25μM), indicating they would have low cytotoxicity when administered as chemical penetration enhancers. The relationships between the lipophilicity and the chemical structure of the studied compounds, as well as the correlation between their chemical structure and transdermal penetration-enhancing activity, are discussed.
- MeSH
- Administration, Cutaneous MeSH
- Hydrophobic and Hydrophilic Interactions MeSH
- Caproates chemistry pharmacology MeSH
- Skin Absorption drug effects MeSH
- Molecular Structure MeSH
- Drug Carriers chemistry MeSH
- Molecular Dynamics Simulation MeSH
- Structure-Activity Relationship MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Ameloblastin (AMBN) was originally believed to be an enamel-specific extracellular matrix glycoprotein secreted by ameloblasts. Recently, AMBN expression was also detected in developing mesenchymal dental hard tissues, in trauma-induced reparative dentin, and during early craniofacial bone formation. The function and structure of AMBN still remain ambiguous, and there are no known proteins with similar primary sequences. We therefore performed a bio-informatic analysis of AMBN to model ab initio the three-dimensional structure of the molecule. The results suggest that AMBN is a two-domain, intrinsically unstructured protein (IUP). The analysis did not reveal any regions with structural similarity to known receptor-ligand systems, and did not identify any higher-order structures similar to functional regions in other known sequences. The AMBN model predicts 11 defined regions exposed on the surface, internalizing the rest of the molecule including a human-specific insert. Molecular dynamics analysis identified one specific and several non-specific calcium-binding regions, mostly at the C-terminal part of the molecule. The model is supported by previous observations that AMBN is a bipolar calcium-binding molecule and hints at a possible role in protein-protein interactions. The model provides information useful for further studies on the function of AMBN.
The role of the dispersion energy and electrostatic energy on the geometry and stability of the B-DNA helix was investigated. Both molecular dynamics simulations with empirical force field and hybrid quantum mechanical/molecular mechanics molecular dynamics simulations, where the dispersion or electrostatics term is suppressed/increased, on the one hand and an ab initio minimization procedure on the other have shown that the lack of the dispersion term leads to an increase of the vertical separation of the bases as well as to a loss of helicity, thus resulting in a ladder-like structure. A decrease of the electrostatic term produces a separation of the DNA strands. The biological consequences of both electrostatic and dispersion forces in DNA are enormous, and without either of them, DNA would become unstable and unable to provide the storage and transfer of genetic information.
Hydration of neutral and cationic imidazole is studied by means of ab initio and molecular dynamics calculations, and by photoelectron spectroscopy of the neutral species in a liquid microjet. The calculations show the importance of long range solvent polarization and of the difference between the structure of water molecules in the first shell around the neutral vs cationic species for determining vertical and adiabatic ionization potentials. The vertical ionization potential of neutral imidazole of 8.06 eV calculated using a nonequilibrium polarizable continuum model agrees well with the value of 8.26 eV obtained experimentally for an aqueous solution at pH 10.6.
