DFT computational study towards investigating Cladribine anticancer drug adsorption on the graphene and functionalized graphene

Structural Chemistry - Density functional theory calculations at the M06-2X/6-31G** level have been carried out to examine the adsorption behavior of Cladribine drug on the graphene and graphene...     

Ab initio study of dielectric response of rippled graphene

Ab initio calculations of dielectric function and electron energy loss (EEL) function of periodically rippled armchair-edged graphene were performed in the framework of the random-phase approximation. The bending of graphene was found to remove restrictions on the electron transitions being forbidden in the flat graphene for certain light polarization. As a result, new peaks appear in the optical absorption spectrum and EEL spectrum of rippled graphene. Energy position, intensity, and width of the peaks are sensitive to the height of out-of-plane graphene bending that can be used in construction of graphene-based materials with variable transparency window.     

Ab initio molecular dynamics study of methanol adsorption on copper clusters

The preferential structures of small copper clusters Cun (n=2-9) and the adsorption of methanol molecules on these clusters are examined with first principles, molecular dynamics simulations. The results show that the copper clusters undergo systematic changes in bond length and bond order associated with altering their preferential structures from one-dimensional structures, to two-dimensional and three-dimensional structures. The results also indicate that low coordination number sites on the copper clusters are both the most favorable for methanol adsorption and have the greatest localization of electronic charge. The simulations predict that charge transfer between the neutral copper clusters and the incident methanol molecules is a key process by which adsorption is stabilized. Importantly, the changes in the dimensionality of the copper clusters do not significantly influence methanol adsorption.     

Ab initio study of the adsorption of NO on the Rh6(+) cluster

The process of NO adsorption on the cationic cluster Rh(6)(+) is investigated using the density-functional theory (DFT) with the generalized gradient approximation (GGA) to exchange and correlation. We determine the geometries, electronic structure, and relevant energies for different structural and spin isomers of Rh(6)(0,±), and we study the consecutive adsorption of two NO molecules on the cationic cluster Rh(6)(+). With regard to the first NO molecule, different adsorption energies are found for the ground state octahedral structure of the bare cationic cluster and for the first isomer, which, having a prism-type structure, undergoes a structural transition to an octahedral symmetry upon dissociative adsorption of NO. Several dissociative NO adsorption processes are analyzed in comparison with molecular adsorption of NO to give support to the first step of the reaction inferred from experiments. With regard to the adsorption of a second NO molecule, the intermediate with lowest energy contains a preformed N(2) molecule. The energy of that complex is about 0.7 eV smaller than the sum of the free N(2) energy plus the lowest energy of the Rh(6)(+)-O(2) complex. This complex is composed of two separated O atoms occupying adjacent 2-fold bridging positions of the nearly undistorted Rh(6)(+) octahedral cluster. These findings are in qualitative agreement with experiments.     

Ab initio study on the adsorption and dissociation process of methanol on a silver surface

The geometries of methanol adsorbed on an oxygen-free silver surface, a promoted silver surface and an oxygen preadsorbed silver surface were optimized at the MP2 level and the energies were calculated at the MP4 level. Our calculations showed that weak physisorption of methanol occurs on the clean silver surface, but stable molecular chemisorption occurs in the other two cases. The adsorption and dissociation process of methanol was postulated to occur via two pathways, i.e. the Eley-Rideal mode and the Langmuir-Hinshelwood mode. The calculations also showed that the presence of atomic oxygen at a silver surface is essential for the cleavage of the OH bond in the methanol. The dissociation of methanol in the Langmuir-Hinshelwood mode has a small energy barrier but has no energy barrier in the Eley-Rideal mode.     

Ab initio study of L-orientational defect in the hydrogen-bonded pattern of liquid water

Current status of the theory of orientational defects in H-bonded pattern of liquid water is briefly reviewed. Ab initio calculated water clusters from dimer to heptamer are thoroughly analyzed in terms of H-bonded pattern. New water heptamer structure of norbornane type is found via ab initio HF 6-311G** calculation. Its normal vibrations are properly assigned. Two ab initio water hexamers that refer to orientational defects are revealed. This is the first evidence of ab initio orientational defect in H-bonded patterns of water clusters. Some properties including normal vibrations of these defects, are studied.     

Ab initio study of molecular oxygen adsorption on Pu (111) surface

Using the generalized gradient approximation to density functional theory (DFT), molecular and dissociative oxygen adsorptions on a Pu (111) surface has been studied in detail. Dissociative adsorption with a layer‐by‐layer alternate spin arrangement of the plutonium layer is found to be energetically more favorable, and adsorption of oxygen does not change this feature. Hor1 (O₂ is parallel to the surface and lattice vectors) approach on the center2 (center of the unit cell, where there is a Pu atom directly below on the third layer) site, both without and with spin polarization, was found to be the preferred chemisorbed site among all cases studied with chemisorption energies of 8.365 and 7.897 eV, respectively. The second‐highest chemisorption energy occurs at the Ver (O₂ is vertical to the surface) approach of the bridge site with chemisorption energies of 8.294 eV (non‐spin‐polarized) and 7.859 eV (spin‐polarized), respectively. We find that 5f electrons are more localized in the spin‐polarized case than the non‐spin‐polarized counterparts. Localization of the 5f electrons is higher in the oxygen‐adsorbed plutonium layers compared with the bare layers. The ionic part of O? Pu bonding plays a significant role in the chemisorption process, along with Pu 5f? O 2p hybridization. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Ab initio study of K adsorption on a Ag(100) surface

Ab initio Hartree–Fock calculations are reported for the chemisorption of K on Ag using three different types of clusters to model the system. Geometry optimization is done in 4 degrees of freedom. It is found that since there is an absence of complete charge transfer between the adsorbate and substrate, the interaction can be interpreted as being predominately covalent in nature.     

Structural photodynamics of camptothecin, an anticancer drug in aqueous solutions

Steady-state and time-resolved picosecond emission studies were carried out to study the role of the proton concentration in the acid-base properties of the anticancer drug camptothecin (CPT) in its ground and electronically first excited states. The results show that, under acidic conditions, the excited-state proton-transfer (ESPT) reaction is irreversible, in contrast to previous literature data. We found that the prototropic species are equilibrated at the excited state (pK(a)* = 1.85) only in a restricted range of pH (1.5 < pH < 3), whereas only one species, either the neutral form (τ(N) = 3.76 ns) or the protonated form (τ(C) = 2.83 ns), can be detected at pH > 3 and pH < 1.5, respectively. The proton motion from the acidic solution to the neutral form in the pH 1-2 domain is diffusion-controlled. Within the range of pH 1-2, the reaction rate constant for the formation (k(d)) of the encounter complex between the proton and the neutral form ranges from 1.17 × 10(10) to 7.33 × 10(10) M(-1) s(-1), respectively. Under more acidic conditions (pH 0.9-0.95), the protonation of CPT does not depend on the diffusive step, because of the large amount of protons. The direct proton-transfer rate constant (k(DPT)*) increases with the proton concentration (time constants change from 24 ps to ～1 ns at pH 0.9 and 2, respectively). The number of protons involved in the proton transfer changes from approximately one, for the diffusive regime, to approximately four, for the static regime. We found good agreement between the Birks model for equilibrated flourophores and the Debye-Smoluchowski equation (DSE) to accurately explain the ESPT reaction of CPT with acidic water in the reversible range. The proton motion at pH 2 (equilibrium range) exhibits diffusion-controlled behavior and can be explained using the Smoluchowski model. Our results show that the interaction of CPT with acidic water depends on the concentration of the acid, which changes the nature of both the structure and dynamics.     

Ab initio theoretical study of non-covalent adsorption of aromatic molecules on boron nitride nanotubes

We have studied non-covalent functionalization of boron nitride nanotubes (BNNTs) with benzene molecule and with seven other different heterocyclic aromatic rings (furan, thiophene, pyrrole, pyridine, pyrazine, pyrimidine, and pyridazine, respectively). A hybrid density functional theory (DFT) method with the inclusion of dispersion correction is employed. The structural and electronic properties of the functionalized BNNTs are obtained. The DFT calculation shows that upon adsorption to the BNNT, the center of aromatic rings tend to locate on top of the nitrogen site. The trend of adsorption energy for the aromatic rings on the BNNTs shows marked dependence on different intermolecular interactions, including the dispersion interaction (area of the delocalized π bond), the dipole-dipole interaction (polarization), and the electrostatic repulsion (lone pair electrons). The DFT calculation also shows that non-covalent functionalization of BNNTs with aromatic rings can give rise to new impurity states within the band gap of pristine BNNTs, suggesting possible carrier doping of BNNTs via selective adsorption of aromatic rings.     

Ab initio and microcalorimetric investigations of alkene adsorption on phosphotungstic acid

The adsorption of ethene, propene, 1-butene, trans-2-butene, and isobutene on phosphotungstic acid has been characterized by density functional theory (DFT) calculations and microcalorimetric experiments. The DFT-calculated chemisorption energies to form the corresponding alkoxides for ethene, propene, 1-butene, trans-2-butene, and isobutene were -86.8, -90.3, -102.6, -79.9, and -91.4 kJ mol(-1), respectively (for their most-favorable binding modes). The relative chemisorption energies to form the alkoxides are dictated by the strength of interaction of the acidic proton with the carbon atom of the double bond that becomes protonated. The activation barrier for chemisorption was greatest for alkenes with primary (1 degrees) carbenium-like transition states followed by secondary (2 degrees) and tertiary (3 degrees) transition states. The adsorption enthalpy established from microcalorimetric experiments with propene and isobutene was approximately -100 kJ mol(-1), which is close to the DFT-calculated values. Chemisorption of ethene on phosphotungstic acid during microcalorimetric experiments was minimal, presumably because of the large activation barrier associated with a 1 degrees carbenium-like transition state. The results from this study are compared with those in the literature for the adsorption of alkenes on zeolites, which have a similar adsorption mechanism. Our results suggest that alkene adsorption is stronger on phosphotungstic acid than on zeolites, as supported by the more exothermic chemisorption energies. Additionally, activation barriers for alkene adsorption are lower over phosphotungstic acid than over zeolites.     

Ab initio study of structural and electronic properties of zigzag graphene nanoribbons on hexagonal boron nitride

Results of the study of structural and electronic properties of the 8-ZGNR/h-BN(001) heterostructure by the pseudopotential method using plane waves within density functional theory are presented. Within one approximation the features of the spin state at the Fermi level are studied along with the role of the edge and substrate effects in the opening of the energy gap in the 8-ZGNR/h-BN(001) heterostructure in both ferromagnetic and antiferromagnetic orderings. The effect of a substrate made of hexagonal boron nitride was found for the first time. It consists in the opening of the energy gap in the π electron spectrum of the 8-ZGNR/h-BN(001) heterostructure for the ferromagnetic spin ordering. It is shown that the gap was 30 meV. Contributions of the edge effects of the graphene nanoribbon and the substrate to the energy gap formation are differentiated for the first time. It is found that in the 8-ZGNR/h-BN(001) heterostructure the dominant role in the opening of the energy gap at the Fermi level is played by the edge effects. However, when the nanoribbon width decreases, e.g., to six dimmers the substrate role in the gap opening increases and amounts to 45%. Local magnetic moments of carbon atoms are estimated. It is shown that small magnetic moments are induced on boron and nitrogen atoms at the interface.     

Ab initio study on cyanamide and isocyanamide

Spectroscopic parameters, namely force constants and dipole-moment derivatives of cyanamide and isocyanamide at their equilibrium geometry, are studied by the ab initio MO method. The configuration of the former of the two structural isomers has amide character, and the latter amine character. The assignments of skeletal-deformation vibrations are reinvestigated experimentally as well. This study supports Ogilvie's attribution of what he observed to the vibrational spectrum of isocyanamide and explains the anomalous infrared intensity in the spectrum. A special theoretical treatment of amino wagging motion is presented, which includes the inversion effect, and which enables the prediction of the inversion splitting of isocyanamide.     

Ab initio study on the adsorption and oxidation of HCHO with Ag2 cluster

We present an ab initio study on the adsorption and oxidation of HCHO on the Ag₂ dimer. HCHO is found to weakly adsorb on the neutral Ag₂ cluster and the adsorption energy increases when the Ag₂ cluster is positively charged. The adsorption of HCHO on Ag₂ is promoted by pre-adsorbed OH species while coadsorbed H has no effect. The formation of η²-methylendioxy is inhibited if the Ag₂ cluster is positively and properly charged, which enhance the selectivity of the partial oxidation of methanol. These results provide insight into the reaction mechanism of HCHO on silver surfaces and may guide the design of novel catalysts.     

Construction of a graphene oxide based noncovalent multiple nanosupramolecular assembly as a scaffold for drug delivery

A multiple supramolecular assembly, in which a folic acid-modified β-cyclodextrin (1) acted as a target unit, an adamantanyl porphyrin (2) acted as a linker unit, and graphene oxide acted as a carrier unit, was successfully fabricated through non-covalent interactions and comprehensively investigated by means of UV/Vis, fluorescence, and X-ray photoelectron spectroscopies, and electron microscopy. Significantly, the graphene oxide unit could associate with the anticancer drug doxorubicin through π-π interactions, and the folic acid-modified β-cyclodextrin unit could recognize the folic acid receptors in cancer cells. Owing to the cooperative contribution of these three units, the resulting multiple supramolecular assembly, after association with doxorubicin, exhibited better drug activity and much lower toxicity than free doxorubicin in vivo.     

Ab initio study of the cyclooctatetraenyl radical

Ab initio calculations have been carried out on the 1,3,5,7- and 1,2,4,7-tetraene configurations of the cyclooctatetraenyl radical at UHF, ROHF, MCSCF, ROCISD, QCISD, and CCSD(T) levels of theory with 6-311G(d,p) and cc-pVDZ basis sets. Although spin contamination is present, the ROCISD calculations support the energies obtained from less intensive, UHF-based coupled cluster calculations over the energies obtained from MCSCF analysis of the pi-electron orbitals. The 1,3,5,7-form is a local minimum at the coupled cluster levels, higher in energy than the resonance-stabilized 1,2,4,7-form by 10-13 kJ/mol, but bounded by a barrier of less than 0.5 kJ/mol. The isomerization surface connecting these two structures is described and results reported from integration of the vibrational Schr?dinger equation on that surface. Excited vibrational states at energies just above the isomerization barrier are dominated by the character of the 1,3,5,7-tetraenyl radical, which suggests that chemistry involving this intermediate at typical combustion temperatures may branch at this juncture.     

用从头算研究Shilov反应的机理

Shilov反应在CH~4活化中占有中心地位,它有氧化加成和σ迁移两种可能的机理。本文用较大基组的从头算研究了这两种机理的反应过程,认为Shilov反应应按氧化加成机理进行。     

Density functional study of hydrogen adsorption and diffusion on Ni‐loaded graphene and graphene oxide

In this work, we performed density functional calculations to investigate the adsorption and diffusion of hydrogen on Ni‐loaded graphene and single layer graphene oxide (SLGO). We evaluated the feasibility of hydrogen spillover in the presence of Ni₄ cluster and the role of oxygen‐containing groups. Our calculations indicate that the hydrogen diffusion is difficult to take place on the Ni/graphene interface due to the stronger Ni? H bond strength. Further, the chemisorbed H atoms are also hard to diffuse freely on the graphene surface. For the SLGO surface, both hydroxyl and epoxide groups may not facilitate the hydrogen diffusion. Instead, they are readily attracted by the nearby Ni catalyst and hydrogenated to water molecules. © 2014 Wiley Periodicals, Inc.     

Ab initio study on the photochemical behavior of styrene

Ab initio complete active space self‐consistent field (CASSCF) and the second order multireference Møller‐Plesset calculations have been performed to examine the photochemical behavior of styrene upon the strong S₀‐S₂ electronic excitation in the low‐lying excited states. The optimized structure at the S₂/S₁ conical intersection (CIX) is characterized by a quinoid structure. The transition state (TS) in S₁ is in the vicinity of the S₂/S₁‐CIX. At the S₁‐TS, two reaction paths branch. One is the relaxation into the stable structure in S₁ and then emission into S₀. The other is the radiationless decay through the S₁/S₀‐CIX. © 2002 Wiley Periodicals, Inc. J Comput Chem 10: 950–956, 2002     

Ab initio study of NH3 and H2O adsorption on pristine and Na-doped MgO nanotubes

We have investigated, on the basis of density functional theory calculations, the structural and electronic properties of chemical modification of pristine and Na-doped MgONTs with NH₃ and H₂O molecules. We found that the NH₃ and H₂O molecules can be barrierlessly adsorbed on the Mg atom of the tube sidewall along with a charge transfer from the adsorbate to MgONT. The adsorption is chemical in nature with adsorption energies about ?22.3 and ?21.5 kcal/mol for H₂O and NH₃, respectively. The calculated density of state (DOS) shows that the chemical modification of MgONTs with these molecules can be generally classified as certain type of “harmless modification.” In other words, the electronic properties of the MgONT are little changed by the adsorption processes. The substitution of an Mg atom in the tube surface with an Na atom results in a semi-insulator to p-type semiconductor transition based on DOS analysis. It was also found that the doping process reduces the adsorption energies and the electronic properties of Na-doped MgONT is slightly more sensitive toward NH₃ and H₂O molecules, compared with the pristine one.