First principles studies of the graphene-phenol interactions

Studies of the interaction between phenol and intrinsic graphene, as well as phenol and aluminum doped graphene layer are performed using first principles total energy calculations within the periodic density functional theory. A 4x4 periodic structure is used to explore the adsorption of a phenol molecule on the intrinsic graphene and on aluminum doped graphene layer. The electron-ion interactions are modeled using ultra-soft pseudo-potentials, and the exchange-correlation energies are treated according to the generalized gradient approximation (GGA) with the PBE parameterization. We consider different molecule orientations: parallel and perpendicular to the graphene layer to relax the atomic structure. To explain the optimized atomic geometry we determine binding energies for all cases and the density of states (DOS) and partial DOS for the most relevant configurations. Results indicate that the direct interaction of oxygen with aluminum yields the ground state geometry with the phenol molecule adsorbed on the graphene layer. Binding energies and DOS structures also demonstrate that the ground state configuration is that where the O and Al atoms interact with a separation distance of 1.97 ?.     

Two-dimensional boron nitride structures functionalization: first principles studies

Density functional theory calculations have been performed to investigate two-dimensional hexagonal boron nitride (2D hBN) structures functionalization with organic molecules. 2x2, 4x4 and 6x6 periodic 2D hBN layers have been considered to interact with acetylene. To deal with the exchange-correlation energy the generalized gradient approximation (GGA) is invoked. The electron-ion interaction is treated with the pseudopotential method. The GGA with the Perdew-Burke-Ernzerhoff (PBE) functionals together with van der Waals interactions are considered to deal with the composed systems. To investigate the functionalization two main configurations have been explored; in one case the molecule interacts with the boron atom and in the other with the nitrogen atom. Results of the adsorption energies indicate chemisorption in both cases. The total density of states (DOS) displays an energy gap in both cases. The projected DOS indicate that the B-p and N-p orbitals are those that make the most important contribution in the valence band and the H-s and C-p orbitals provide an important contribution in the conduction band to the DOS. Provided that the interactions of the acetylene with the 2D layer modify the structural and electronic properties of the hBN the possibility of structural functionalization using organic molecules may be concluded.     

Effect of the Si,Al and B doping on the sensing behaviour of carbon nanotubes toward ethylene oxide: a computational study

ABSTRACT

Exo– and endo–adsorption of ethylene oxide (EO) on pristine (9,0) (zigzag) carbon nanotube (CNT) and its doped forms with silicon (Si–CNT), aluminum (Al–CNT) and boron (B–CNT) were investigated using density functional theory (DFT) at M06–2X/6–311++G** level. The natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) analyses were also performed by using the same level of theory. The effect of the doping on sensing behaviour of the CNT toward EO molecule was investigated through intermolecular interactions studies by calculation of total and partial density of states (DOS, PDOS). The enhanced sensitivity of doped–CNTs towards EO molecule associated with adsorption energies (E_ads) and the changes in geometric and electronic structures was examined and the global chemical reactivity parameters were calculated and comprehensively analysed. The thermodynamic property changes were calculated and compared. The results indicated that the EO adsorption on the pristine and doped CNTs was an exothermic spontaneous process. Moreover, based on the calculated E_g change (ΔE_g) and E_ads values, Al–CNT with superior sensitivity for sensing of EO molecule, indicates promising perspectives for its use in fabrication of new EO gas–sensing devices.     

Interaction between an icosahedron Li13 cluster and a graphene layer doped with a hydrogen atom

It is known that graphene reacts with atomic hydrogen to form a hydrogenated sheet of graphene. In order to understand the nature of the interaction between hydrogen and lithium in hydrogenated samples, we have carried out first principle calculations. Density functional theory and molecular dynamics were used to study the interaction between an icosahedron Li₁₃ cluster, and a graphene layer doped with a hydrogen atom. It was found that a hydrogen atom is levitated from the graphene layer and absorbed into the cluster of Li at 300?K and atmospheric pressure, with a binding energy far exceeding that of the adsorption energy of a hydrogen atom on the graphene layer.     

Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy

BtrN is a radical SAM ( S-adenosyl- l-methionine) enzyme that catalyzes the oxidation of 2-deoxy- scyllo-inosamine (DOIA) into 3-amino-2,3-dideoxy- scyllo-inosose (amino-DOI) during the biosynthesis of 2-deoxystreptamine (DOS) in the butirosin producer Bacillus circulans. Recently, we have shown that BtrN catalyzes the transfer of a hydrogen atom at C-3 of DOIA to 5'-deoxyadenosine, and thus, the reaction was proposed to proceed through the hydrogen atom abstraction by the 5'-deoxyadenosyl radical. In this work, the BtrN reaction was analyzed by EPR spectroscopy. A sharp double triplet EPR signal was observed when the EPR spectrum of the enzyme reaction mixture was recorded at 50 K. The spin coupling with protons partially disappeared by reaction with [2,2- (2)H 2]DOIA, which unambiguously proved the observed signal to be a radical on C-3 of DOIA. On the other hand, the EPR spectrum of the [4Fe-4S] cluster of BtrN during the reaction showed a complex signal due to the presence of several species. Comparison of signals derived from a [4Fe-4S] center of BtrN incubated with various combinations of products (5'-deoxyadenosine, l-methionine, and amino-DOI) and substrates (SAM and DOIA) indicated that the EPR signals observed during the reaction were derived from free BtrN, a BtrN-SAM complex, and a BtrN-SAM-DOIA complex. Significant changes in the EPR signals upon binding of SAM and DOIA suggest the close interaction of both substrates with the [4Fe-4S] cluster.     

The stereochemistry of biosynthesis of decaprenoxanthin in a cell-free system

Intact cells of Flavobacterium dehydrogenans grown on glucose or acetate did not incorporate mevalonic acid-[¹⁴C]. After treatment with lysozyme the protoplasts were lysed by sonication in a dilute medium containing mevalonic acid-[¹⁴C] and the cell-free system produced incorporated label into uncyclized C₄₀, monocyclic C₄₅ and bicyclic C₅₀ carotenoids of which decaprenoxanthin was the most abundant.With mevalonate-[2-¹⁴C,4R-4-³H₁] the ¹⁴C:³H ratios of the carotenoids showed that the hydrogen atoms at C-2 and C-6 of the ring and that at C-3 of the 1-hydroxy, 2-methyl but-2-ene-4-yl residues of decaprenoxanthin were derived from the 4-pro-R hydrogen atom of mevalonic acid.Mevalonate-[2-¹⁴C,2R-2-³H₁] and mevalonate-[2-¹⁴C,2S-2-³H₁] gave ratios which showed that the C-4 hydrogen atoms of decaprenoxanthin were derived from the 2-pro-S hydrogen atom of mevalonic acid.     

Studies in phytosterol biosynthesis. Mechanism of biosynthesis of cycloartenol

1. The mechanism of cycloartenol biosynthesis in leaves of Solanum tuberosum was investigated with the use of [2-¹⁴C,(4R)-4-³H₁]mevalonic acid. 2. The ³H/¹⁴C atomic ratio in cycloartenol was 6:6, the same as that in squalene; this eliminates lanosterol as a possible biosynthetic precursor of cycloartenol, and indicates that a hydrogen migration from C-9 to C-8 occurs. 3. Chemical isomerization of the cycloartenol to lanosterol (³H/¹⁴C ratio 5:6) and parkeol (³H/¹⁴C ratio 6:6) confirms the hydrogen migration from C-9 to C-8. 4. Possible mechanisms for the biosynthesis of cycloartenol and parkeol are discussed. 5. The ³H/¹⁴C ratio for 24-methylenecycloartanol was 6:6, demonstrating that the hydrogen atom at C-24 is retained during alkylation of the cycloartenol side chain.     

Cluster Approach of Active Sites in an MoS2 Catalyst

The present paper reports a Density Functional Theory (DFT) study of a Mo₁₂S₂₄ cluster as a model of the active phase in hydrodesulphurisation (HDS). Different types of sulphur vacancies are considered and compared. The interaction of a thiophene molecule with a double vacancy is simulated leading to the determination of a stable configuration which corresponds to a flat adsorption on the edge of the MoS₂ sheets. The dissociative adsorption of molecular hydrogen on a double vacancy is also considered.Electronic Supplementary Material available.     

Evidence for a C-2→C-1 intramolecular hydrogen-transfer during the acid-catalyzed isomerization of D-glucose to D-fructose ag]

In mechanistic studies by isotope-exchange tecniques of the conversion of D-fructose and D-glucose into 2-(hydroxyacetyl)furan, it was shown that both sugars are converted in acidified, tritiated water into the furan containing essentially no carbon-bound tritium. As the hydroxymethyl carbon atom of the furan corresponds to C-1 of the hexose, this result suggests that one of the hydrogen atoms in this group, when it is produced from D-glucose, must arise intramolecularly. This hypothesis was verified by synthesizing D-glucose-2-³H and converting it into the furan in acidified water. The 2-(hydroxyacetyl)furan obtained was labeled exclusively on the hydroxymethyl carbon atom, thus showing that intramolecular hydrogen-transfer occurs, during the conversion, from C-2 of D-glucose to the carbon atom corresponding to C-1. The specific activities of the product and reactant permitted calculation of the tritium isotope-effect (k_h/k_t=4.4) for the reaction. The precise step for the transfer from C-2 of the aldose to the carbon atom corresponding to C-1 was found to be during the isomerization of D-glucose to D-fructose, as evidenced by the conversion of D-glucose-2-³H into D-fructose-1-³H in acidified water.     

Hydrogen sequential dissociative chemisorption on Nin(n = 2~9,13) clusters: comparison with Pt and Pd

Hydrogen dissociative chemisorption and desorption on small lowest energy Ni_n clusters up to n = 13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy path calculations suggest that H₂ dissociative chemisorption is both thermodynamically and kinetically favorable and the H atoms on the clusters are mobile. Calculations on the sequential H₂ dissociative chemisorption on the clusters indicate that the edge sites are populated first and subsequently several on-top sites and hollow sites are also occupied upon full cluster saturation. In all cases, the average hydrogen capacity on Ni_n clusters is similar to that of Pd_n clusters but considerably smaller than that of Pt_n clusters. Comparison of hydrogen dissociative chemisorption energies and H desorption energies at full H-coverage among the Ni family clusters was made.     

Density functional study of H<Subscript>2</Subscript>O molecule adsorption on α-U(001) surface

Periodic density functional theory (DFT) calculations were performed to investigate the adsorption of H₂O on U(001) surface. The metallic nature of uranium atom and different adsorption sites of U(001) surface play key roles in the H₂O molecular dissociate reaction. The long-bridge site is the most favorable site of H₂O-U(001) adsorption configuration. The triangle-center site of the H atom is the most favorable site of HOH-U(001) adsorption configuration. The interaction between H₂O and U surface is more evident on the first layer than that on any other two sub-layers. The dissociation energy of one hydrogen atom from H₂O is ?1.994 to ?2.215 eV on U(001) surface, while the dissociating energy decreases to ?3.351 to ?3.394 eV with two hydrogen atoms dissociating from H₂O. These phenomena also indicate that the O_ads can promote the dehydrogenation of H₂O. A significant charge transfer from the first layer of the uranium surface to the H and O atoms is also found to occur, making the bonding partly ionic.     

Stereochemistry of phytoene biosynthesis by isolated chloroplasts

The incorporation of [2-(14)C,(5R)-5-(3)H(1)]MVA* and [2-(14)C,5-(3)H(2)]MVA into geranylgeraniol and phytoene by a preparation of ;non-aqueous' bean leaf chloroplasts has been studied. In the formation of phytoene from two molecules of geranylgeranyl pyrophosphate, the loss of hydrogen is stereospecific, the hydrogen atom lost from C-1 of each molecule of geranylgeranyl pyrophosphate being that which was originally the pro-S hydrogen atom from C-5 of mevalonate. All the pro-R hydrogen atoms from C-5 of mevalonate are retained. These results with a cell-free system confirm and extend the observations made in previous work with tomato slices.     

Evidence for a C-2→C-1 intramolecular hydrogen-transfer during the acid-catalyzed isomerization of D-glucose to D-fructose ag]

In mechanistic studies by isotope-exchange tecniques of the conversion of D-fructose and D-glucose into 2-(hydroxyacetyl)furan, it was shown that both sugars are converted in acidified, tritiated water into the furan containing essentially no carbon-bound tritium. As the hydroxymethyl carbon atom of the furan corresponds to C-1 of the hexose, this result suggests that one of the hydrogen atoms in this group, when it is produced from D-glucose, must arise intramolecularly. This hypothesis was verified by synthesizing D-glucose-2-³H and converting it into the furan in acidified water. The 2-(hydroxyacetyl)furan obtained was labeled exclusively on the hydroxymethyl carbon atom, thus showing that intramolecular hydrogen-transfer occurs, during the conversion, from C-2 of D-glucose to the carbon atom corresponding to C-1. The specific activities of the product and reactant permitted calculation of the tritium isotope-effect (k_h/k_t4.4) for the reaction. The precise step for the transfer from C-2 of the aldose to the carbon atom corresponding to C-1 was found to be during the isomerization of D-glucose to D-fructose, as evidenced by the conversion of D-glucose-2-³H into D-fructose-1-³H in acidified water.     

Fluorination of BC3 nanotubes: DFT studies

We have studied the adsorption of atomic and molecular fluorines on a BC₃ nanotube by using density functional calculations. It was found that the adsorption of atomic fluorine on a C atom of the tube surface is energetically more favorable than that on a B atom by about 0.97 eV. The adsorption of atomic fluorine on both C and B atoms significantly affects the electronic properties of the BC₃ tube. The HOMO-LUMO energy gap is considerably reduced from 2.37 to 1.50 and 1.14 eV upon atomic F adsorption on B and C atoms, respectively. Molecular fluorine energetically tends to be dissociated on B atoms of the tube surface. The associative and dissociative adsorption energies of F₂ were calculated to be about ?0.42 and ?4.79 eV, respectively. Electron emission density from BC₃ nanotube surface will be increased upon both atomic and molecular fluorine adsorptions due to work function decrement.     

Transition metal doped ZnO nanoclusters for carbon monoxide detection: DFT studies

Metal doped ZnO nanomaterials have attracted considerable attention as a chemical sensor for toxic gases. Here, the electronic sensitivity of pristine and Sc-, Ti-, V-, Cr-, Mn-, and Fe-doped Zn₁₂O₁₂ nanoclusters toward CO gas is investigated using density functional theory calculations. It is found that replacing a Zn atom by a Sc or Ti atom does not change the sensitivity of cluster but doping V and Cr atoms significantly increase the sensitivity. Also, Mn, or Fe doping slightly improves the sensitivity. It is predicted that among all, the Cr-doped ZnO cluster may be the most favorable sensor for CO detection because its electrical conductivity considerably changes after the CO adsorption, thereby, generating an electrical signal. The calculated Gibbs free energy change for the adsorption of CO molecule on the Cr-doped cluster is about -51.2 kcal mol^-1 at 298.15 K and 1 atm, and the HOMO-LUMO gap of the adsorbent is changed by about 117.8 %.     

Evidence for geraniol as an obligatory precursor of isothujone

Isothujone (trans-thujan-3-one) was formed from MVA-[¹⁴C, ³H] in Tanacetum vulgare with retention of the pro-(4R) hydrogen of precursor, but with loss of the pro-(4S) hydrogen and of one hydrogen from C-5. Cell-free extracts could not sustain the formation of isothujone from MVA but yielded geraniol and nerol (3,7-dimethylocta-trans-2,6-dien-1-ol and its cis isomer) with retention of the pro-(4R) and loss of the pro-(4S) hydrogen in each case: no hydrogen was lost from C-5 of MVA in formation of geraniol, but one such atom was lost in the formation of nerol. These results support the sequence: geraniol → nerol → isothujone: in which the first two compounds (or their biogenetic equivalents) are interconverted by a redox process involving their derived aldehydes. They are not consistent with a direct pathway to nerol from C₅ intermediates or with routes involving cyclisation of linalol (3,7-dimethylocta-1,6-dien-3-ol) formed directly from the C₅ compounds or from geraniol. The cell-free preparations could not interconvert geraniol and nerol, their phosphates or pyrophosphates. This may be due to the inability of a prenyltransferase-isomerase multi-enzyme system to accept exogenously-supplied intermediates under these (in vitro) conditions.     

The transfer of hydrogen from C-24 to C-25 in ergosterol biosynthesis

1. A convenient synthesis of 3-hydroxytrisnorlanost-8-en-24-al and its conversion into [24-(3)H]lanosterol and [26,27-(14)C(2)]lanosterol is described. 2. A method for the efficient incorporation of lanosterol into ergosterol by the whole cells of Saccharomyces cerevisiae is also described. 3. It is shown that in the biosynthesis of ergosterol from doubly labelled lanosterol the C-24 hydrogen atom of lanosterol is retained in ergosterol. 4. On the basis of unambiguous degradations it is shown that the C-alkylation step in ergosterol biosynthesis is accompanied by the migration of a hydrogen atom from C-24 to C-25. 5. The mechanism for the biosynthesis of the ergosterol side chain is presented. 6. Mechanisms of other C-alkylation reactions are also discussed.     

Structure-activity relationship on (+/-)-nantenine derivatives in antiserotonergic activities in rat aorta

A series of nine (+/-)-nantenine derivatives were synthesized and assayed for their pharmacological activities by using tension in aorta and binding experiments in rat brain membrane. Replacing a methyl group with a hydrogen ((+/-)-nornantenine) and an ethyl group at a nitrogen atom ((+/-)-ethylnornantenine) or introducing a hydroxyl group at the alpha/beta position of C-4 or displacement of a methoxy moiety at the C-1 position with a hydroxyl ((+/-)-domesticine) of (+/-)-nantenine decreased the affinity. Moreover, changing a methyl group of (+/-)-domesticine to hydrogen at a nitrogen atom ((+/-)-nordomesticine) caused loss of the activities. These results suggest that a methyl group at a nitrogen atom and a methoxy moiety at C-1 play important roles in the development of the antiserotonergic activity. Molecular modeling analysis of the interaction between the 5-HT2A receptor and (+/-)-nantenine suggested that electron lone pairs of N-6 and of the oxygen atom of the methoxy group at C-1 are important in forming a hydrogen bond to Asp155 and Asn343 of the 5-HT2A receptor, respectively.     

Selective deuterium labeling of the sphingoid backbone: facile syntheses of 3,4,5-trideuterio-d-erythro-sphingosine and 3-deuterio-d-erythro-sphingomyelin

Deuteration at C-4 and C-5 of sphingosine was achieved via a hydrogen–deuterium exchange reaction of a β-ketophosphonate intermediate catalyzed by ND₄Cl in D₂O/tetrahydrofuran. To install deuterium at C-3 of sphingosine and sphingomyelin, sodium borodeuteride reduction/cerium(III) chloride reduction of an α,β-enone in perdeuteromethanol was used.     

The allomerization of chlorophylls a and b with superoxide anion

The interaction of chlorophylls a and b with electrochemically prepared superoxide anion was studied in aprotic solvent. It was found that O₂^?·causes the deprotonation at carbon C-10 of ring V and production of chlorophyll enolate ions. The intermediate anions undergo rapid oxidation into corresponding chlorins. Pyrochlorophyll a, which lacks the C-10 carboxymethyl group, did not show the transformation. It is suggested that more strong free radical oxidants (e.g., HO₂·, or RO₂·) are capable of abstracting the hydrogen atom at C-10. The possible significance of free radical deprotonation and oxidation in chlorophyll allomerization is discussed.