DFT study of CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O co-adsorption on carbon models of coal surface

The moisture content of coal affects the adsorption capacity of CO₂ on the coal surface. Since the hydrogen bonds are formed between H₂O and oxygen functional group, the H₂O cluster more easily adsorbs on the coal micropore than CO₂ molecule. The coal micropores are occupied by H₂O molecules that cannot provide extra space for CO₂ adsorption, which may leads to the reduction of CO₂ adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO₂ and adsorbed H₂O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H₂O to CO₂ adsorption. This study reports some typical coal-H₂O···CO₂ complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H₂O molecule can more stably adsorb on the aromatic ring surface than CO₂ molecule, and the absolute values of local ESP maximum and minimum of H₂O cluster are greater than CO₂. AIM analysis shows a detailed interaction path and strength between atoms in CO₂ and H₂O, and RDG analysis shows that the interactions among CO₂, H₂O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO₂ and H₂O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H₂O can promote CO₂ adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO₂ adsorption capacity, the attractive interaction of adsorbed H₂O to CO₂ makes little contribution.     

Density functional theory investigation of cocaine water complexes

Twenty cocaine–water complexes were studied using density functional theory (DFT) B3LYP/6-311++G** level to understand their geometries, energies, vibrational frequencies, charge transfer and topological parameters. Among the 20 complexes, 12 are neutral and eight are protonated in the cocaine-water complexes. Based on the interaction energy, the protonated complexes are more stable than the neutral complexes. In both complexes, the most stable structure involves the hydrogen bond with water at nitrogen atom in the tropane ring and C?=?O groups in methyl ester. Carbonyl groups in benzoyl and methyl ester is the most reactive site in both forms and it is responsible for the stability order. The calculated topological results show that the interactions involved in the hydrogen bond are electrostatic dominant. Natural bond orbital (NBO) analysis confirms the presence of hydrogen bond and it supports the stability order. Atoms in molecules (AIM) and NBO analysis confirms the C-H?·?·?·?O hydrogen bonds formed between the cocaine-water complexes are blue shifted in nature.     

Revealing substitution effects on the strength and nature of halogen-hydride interactions: a theoretical study

A quantum chemistry study was carried out to investigate the strength and nature of halogen bond interactions in HXeH···XCCY complexes, where X = Cl, Br and Y = H, F, Cl, Br, CN, NC, C₂H, CH₃, OH, SH, NH₂. Examination of the electrostatic potentials V(r) of the XCCY molecules reveals that the addition of substituents has a significant effect upon the most positive electrostatic potential on the surface of the interacting halogen atom. We found that the magnitude of atomic charges and multipole moments depends upon the halogen atom X and is rather sensitive to the electron-withdrawing/donating power of the remainder of the molecule. An excellent correlation was found between the most positive electrostatic potentials on the halogen atom and the interaction energies. For either HXeH···ClCCY or HXeH···BrCCY complexes, an approximate linear correlation between the interaction energies and halogens multipole moments are established, indicating that the electrostatic and polarization interactions are responsible for the stability of the complexes. According to energy decomposition analysis, it is revealed that the electrostatic interactions are the major source of the attraction in the HXeH···XCCY complexes. Furthermore, the changes in the electrostatic term are mainly responsible for the dependence of interaction energy on the halogen atom.

Cooperativity between fluorine-centered halogen bonds: investigation of substituent effects

This article analyzes the substitution effects on cooperativity between fluorin-centered halogen bonds in NCF?·?·?·?NCF?·?·?·?NCX and CNF?·?·?·?CNF?·?·?·?CNX complexes, where X?=?H, F, Cl, CN, OH, and NH₂. These effects are investigated theoretically in terms of geometric and energetic features of the complexes, which are computed by ab initio methods. The topological analysis, based on the quantum theory of atoms in molecules (QTAIM), is used to characterize the interactions and analyze their enhancement with varying electron density at bond critical points. It is found that the complexes with electron-donating groups exhibit a strong cooperativity, while a much weaker cooperativity occurs in the NCF?·?·?·?NCF?·?·?·?NCCN and CNF?·?·?·?CNF?·?·?·?CNCN trimers. An excellent correlation is found between the cooperative energy in the ternary complexes and the calculated three-body interaction energies. The energy decomposition analysis (EDA) indicates that the electrostatic and dispersion effects play a main role in the cooperativity of fluorine-centered halogen bonding.

Anesthetic-protein interaction Random versus helix polylysine monolayers and interaction with 1-alkanols

Penetration of 1-alkanols into monolayers of hydrophobic polypeptides, poly(ε-benzyloxycarbonyl-l-lysine) and poly(ε-benzyloxycarbonyl-dl-lysine), was compared with their adsorption on the air/water interface in the absence of monolayers. The polypeptide prepared from l-lysine is generally considered to be in the α-helical form whereas dl-copolymer polypeptide contains random-coiled portions due to the structural incompatibility between the two isomers. The free energy of adsorption of 1-alkanols on the air/water interface at dilute concentrations was ?0.68 kcal·mol^?1 per methylene group and 0.15 kcal·mol^?1 for the hydroxyl group at 25°C. In the close-packed state, the surface area occupied by each molecule of 1-alkanols of varying carbon chain-lengths showed nearly a constant value of about 27.2 Ų, indicating perpendicular orientation of the alkanol molecules at the interface. About 75% of the water surface was covered by 1-butanol in this close-packed state. The mode of adsorption of 1-alkanols on the vacant air/water interface followed the Gibbs surface excess while the mode on the polypeptide membranes followed the Langmuir adsorption isotherm, indicating that the latter is characterized by the presence of a finite number of binding sites. The free energies of adsorption of 1-alkanols on the l-polymer monolayers were more negative than those on the vacant air/water interface and less negative than those on the dl-copolymer monolayers. Thus, the affinity of 1-alkanols to the interface was in the order of vacant air/water interface <l-polymer <dl-copolymer. The difference between the air/water interface and l-polymer was about 0.54 kcal·mol^?1 and that between l-polymer and dl-copolymer was 0.17 kcal·mol^?1 at 25°C: the adsorption of 1-alkanols to the dl-copolymer was favored compared to the l-polymer. The polar moieties of the backbone of the dl-copolymer may be exposed to the aqueous phase at the disordered portion. Dipole interaction between this portion and 1-alkanol molecules may account for the enhanced adsorption of the alkanols to the dl-copolymer.     

A DFT study of adsorption and decomposition of hexahydro-1,3,5-trinitro-1,3,5-triazine on Mg(0001) surface

The adsorption and decomposition of hexogen (RDX) molecule on the Mg(0001) surface were investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employed a supercell (4?×?4?×?4) slab model and three-dimensional periodic boundary conditions. The strong attractive forces between RDX molecule and magnesium atoms induce the RDX’s N???O bond breaking. Subsequently, the dissociated oxygen atoms and radical fragment of RDX oxidize the Mg surface. The largest adsorption energy is ?2104.0 kJ mol^-1. We also investigated the decomposition mechanism of RDX molecule on the Mg(0001) surface. The activation energy for the dissociation step of configuration V4 is as small as 2.5 kJ mol^-1, while activation energies of other configurations are much larger, in the range of 964.9–1375.1 kJ mol^-1. Mg powder is more active than Al powder, and Mg powder performs better in increasing the combustion exothermicity of RDX as well.     

Exohedral and endohedral adsorption of alkaline earth cations in BN nanocluster

Adsorption of three alkaline earth cations inside and outside of a B₁₂N₁₂ nano-cage in aqueous medium was investigated using density functional theory. The results obtained are discussed in terms of thermodynamic, geometric, and electronic properties. Based on the calculation of enthalpy changes at 298 K and 1 atm, the adsorption of the considered cations was found to be exothermic outside the cluster while it is endothermic inside. It was also found that the exohedral adsorption favorability of the cluster increases in the series: Ca²⁺?<?Mg²⁺?<<?Be²⁺ with Gibbs free energy changes in the range of ?0.08 to ?1.53 eV at B3LYP/6-31G (d) level of theory. Overall, interaction of the cations with the cluster influences the electronic properties of the cluster through stabilizing the HOMO and LUMO as well as reducing the energy gap between them. However, the electronic properties changed much more in the case of endohedral adsorption in comparison with the exohedral adsorption.     

Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite

Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.     

Efficient adsorptive removal of Congo red from aqueous solution by synthesized zeolitic imidazolate framework-8

Dyes exposure in aquatic environment creates risks to human health and biota due to their intrinsic toxic mutagenic and carcinogenic characteristics. In this work, a metal-organic frameworks materials, zeolitic imidazolate framework-8 (ZIF-8), was synthesized through hydrothermal reaction for the adsorptive removal of harmful Congo red (CR) from aqueous solution. Results showed that the maximum adsorption capacity of CR onto ZIF-8 was ultrahigh as 1250 mg g^?1. Adsorption behaviors can be successfully fitted by the pseudo-second order kinetic model and the Langmuir isotherm equation. Solution conditions (pH condition and the co-exist anions) may influent the adsorption behaviors. The adsorption performance at various temperatures indicated the process was a spontaneous and endothermic adsorption reaction. The enhanced adsorption capacity was determined due to large surface area of ZIF-8 and the strong interactions between surface groups of ZIF-8 and CR molecules including the electrostatic interaction between external active sites Zn?OH on ZIF-8 -and ?SO₃ or –N=N– sites in CR molecule, and the π–π interaction.     

Theoretical study of chemisorption of cyanuric fluoride and S-triazine on the surface of Al-doped graphene

We studied the adsorption of cyanuric fluoride (CF) and s-triazine (ST) molecules on the surface of pristine as well as Al-doped graphenes using density functional theory calculations. Our results reveal low adsorption on the surface of pristine graphene; but by modification of surface using aluminium, resulted Al-doped graphene becomes more reactive towards both CF and ST molecules. We aimed to focus on the adsorption energy, electronic structure, charge analysis, density of state and global indices of each system upon adsorption of CF and ST molecules on the above-mentioned surfaces. Our calculated adsorption energies for the most stable position configurations of CF and ST on Al-doped graphene were ?76.53 kJ mol^?1 (?57.45 kJ mol^?1 BSSE corrected energy) and ?115.55 kJ mol^?1 (?86.87 kJ mol^?1 BSSE corrected energy), respectively, which point to the chemisorption process. For each CF and ST molecule, upon adsorption on the surface of Al-doped graphene, the band gap of HOMO-LUMO was reduced considerably and it becomes a p-type semiconductor, whereas there is no hybridisation between the above-mentioned molecules and pristine graphene.     

Adsorption and decomposition mechanism of hexogen (RDX) on Al(111) surface by periodic DFT calculations

The adsorption of hexogen (RDX) molecule on the Al(111) surface was investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employ a supercell (4×4×3) slab model and three-dimensional periodic boundary conditions. The strong attractive forces between RDX molecule and aluminum atoms induce the N?O and N?N bond breaking of the RDX. Subsequently, the dissociated oxygen atoms, NO₂ group and radical fragment of RDX oxidize the Al surface. The largest adsorption energy is ?835.7 kJ mol^–1. We also investigated the adsorption and decomposition mechanism of RDX molecule on the Al(111) surface. The activation energy for the dissociation steps of V4 configuration is as large as 353.1 kJ mol^–1, while activation energies of other configurations are much smaller, in the range of 70.5–202.9 kJ mol^–1. The N?O is even easier than the N?NO₂ bond to decompose on the Al(111) surface.     

Computational investigation of the adsorption of carbon dioxide onto zirconium oxide clusters

A theoretical investigation of the adsorption of CO(2) onto ZrO(2) is presented. Various cluster models were used to mimic different basic and acidic sites on the surface. The method used was the density functional theory with the generalized gradient approximation and including Grimme's empirical model in order to properly describe the weak interactions that may occur between the adsorbate and the surface. We found that the adsorption at sites exhibiting two adjacent unsaturated zirconium atoms led to either the exothermic dissociation of CO(2) or to a strongly physisorbed state. By contrast, on a single unsaturated zirconium, CO(2) was adsorbed in an apical manner. In this case, the molecule is highly polarized and the adsorption energy amounts to -64.6?kJ?mol(-1). Finally, the weakest adsorption of CO(2) occurred on the basic OH sites on the surface.     

Kinetics of adsorption of globular proteins at an air-water interface.

Adsorption of globular proteins at an air-water interface from an infinite stagnant medium was modeled as one-dimensional diffusion in a potential field. The interaction potential experienced by an adsorbing molecule consisted of contributions from electrostatic interactions, work done against the surface pressure to clear area at the interface in order to anchor the adsorbed segments, and the change in the free energy due to exposure of penetrated surface hydrophobic functional groups to air. The assumption of irreversible adsorption is employed in the present analysis. The energy barrier to adsorption, present at sufficiently large surface pressures, was found to be higher for smaller surface hydrophobicities, larger surface pressures, larger size molecules, and oblate orientation of an ellipsoidal molecule. Consequently, more adsorption occurred at larger surface hydrophobicities, smaller size molecules, and for prolate orientation of ellipsoidal molecules. The subphase concentration has been shown to be zero at short times, increasing with time at larger times, and eventually becoming close to the bulk concentration as a result of increasing energy barrier to adsorption. The predicted evolution of surface concentration with time for adsorption of lysozyme at an air-water interface agreed well with the experimental data of Graham and Phillips (1979a).     

Ab initio molecular dynamics simulations of the adsorption of the methylguanidine or methylguanidinium on Ag(111)

A density-functional and Car–Parrinello molecular dynamics methods were employed to study the adsorption of the methylguanidine or methylguanidinium on Ag(111) surface with Vanderbilt pseudopotentials and PBE functional. The geometry, interacting energy, vibrational frequency, Mayer bond order and electrostatic fit charges were calculated. The results show that the methylguanidine interacts with the Ag(111) surface mainly through the interaction between the sp² hybridisation imine nitrogen and its nearest silver atom on top site, assisted with the Ag???H interaction, with the most stabilising interacting energy ?78.83 kJ/mol. The Car–Parrinello molecular dynamics results at 293.15 or 300.00 K indicate that the Ag???N interaction exists stably for more than 6 ps and the Mayer bond order analysis shows that it is the main interaction in adsorption. For the methylguanidinium on Ag(111) surface, the weak interaction between N?H and its neighbour silver atoms, with the energy of ?40.73–?42.68 kJ/mol and the interacting time of 0.2–0.3 ps at 300 K, could not keep it steady on Ag(111). The CP dynamics results show that only the methylguanidine could adsorb on Ag(111) at the room temperature.     

Do coinage metal anions interact with substituted benzene derivatives?

The nature of the anion–π interaction has been investigated by carrying out ab initio calculations of the complexes of coinage metal anions (Au^?, Ag^?, and Cu^?) with different kinds of π-systems. The binding energies indicate that gold anion has the highest and copper anion has the lowest affinity for interactions with π-systems. Different aspects of the anion–π interaction in these systems have been investigated, including charge-transfer effects (using the Merz–Kollman method), “atoms-in-molecules” (AIM) topological parameters, and interaction energies (using energy decomposition analysis, EDA). Our results indicated that, for most M^?···π interactions, the electrostatic term provides the dominant contribution, whereas polarization, charge transfer, and dispersion effects contribute less than 25 % of the interaction. We believe that the present results should lead to a greater understanding of the basis for anion–π interactions of coinage metal anions.     

Effect of stepwise microhydration on the methylammonium···phenol and ammonium···phenol interaction

A computational study has been performed for studying the characteristics of the interaction of phenol with ammonium and methylammonium cations. The effect of the presence of water molecules has also been considered by microhydrating the clusters with up to three water molecules. Clusters of phenol with ammonium and methylammonium cations present similar characteristics, though ammonium complexes have been found to be more stable than the methylammonium ones. The first water molecule included in the complexes interacts with a N-H group of ammoniun cations and simultaneously with the hydroxyl oxygen atom of phenol (or the aromatic ring). This first water molecule is more tightly bound in the complex, so the stability gain as more water molecules are included drops significantly by 2-3 kcal?mol^?1 with respect to the first one. As more water molecules are included, the differences between favorable coordination sites (the cation, the hydroxyl group or a previous water molecule) decrease. As a consequence, several of the most stable complexes located including three water molecules already exhibit hydrogen bonds between the hydroxyl group and one water molecule. The results indicate that a cyclic pattern formed by a series of hydrogen bonds: π···H-N-H···O-H···O-?, is characteristic of the most stable minima, being kept as more water molecules are included in the system. Therefore, this pattern can be expected to be crucial in ammonium cations···phenol interaction if exposed to the solvent to any degree.     

Winter condition of marine plankton populations in Saanich inlet,B.C., canada. I. Phytoplankton and its surrounding environment

Weekly sampling was carried out in Saanich Inlet, British Columbia throughout the winter of 1975–1976. The surface water column was characterized by exposure to low solar radiation energy (<150 g cal·cm^?2 · day^?1), slight stratification with occasional vertical mixing, and abundant algal nutrients. Phytoplankton were mostly distributed above 5 m in the water column, with a fairly low biomass averaging <1 μgchla·1^?1. Dominant phytoplankton organisms were nanoflagellates occasionally accompanied by dinoflagellates as the second dominant. Centric diatoms, which were dominant in the blooms, were always present but less than a few percentage of the total phytoplankton biomass. Daily photosynthetic productivity was exclusively limited by available radiant energy. Low solar radiation and occasional mixing of the surface zone prohibited the centric diatoms from becoming dominant.     

Molecular dynamics study of small PNA molecules in lipid-water system

We present the results of molecular dynamics simulations of small peptide nucleic acid (PNA) molecules, synthetic analogs of DNA, at a lipid bilayer in water. At neutral pH, without any salt, and in the NP(n)gammaT ensemble, two similar PNA molecules (6-mers) with the same nucleic base sequence and different terminal groups are investigated at the interface between water and a 1-palmitoyl-2-oleoylphosphatidylcholine lipid bilayer. The results of our simulations suggest that at low ionic strength of the solution, both PNA molecules adsorb at the lipid-water interface. In the case where the PNA molecule has charged terminal groups, the main driving force of adsorption is the electrostatic attraction between the charged groups of PNA and the lipid heads. The main driving force of adsorption of the PNA molecule with neutral terminal groups is the hydrophobic interaction of the nonpolar groups. Our simulations suggest that the system free energy change associated with PNA adsorption at the lipid-water interface is on the order of several tens of kT per PNA molecule in both cases.