The catalytic pyrolysis pathways of carbonyl compounds in coal were systematically studied using density functional theory (DFT), with benzaldehyde (C6H5CHO) employed as a coal-based model compound and ZnO, γ-Al2O3, and CaO as catalysts. The results show that the products of both pyrolysis and catalytic pyrolysis are C6H6 and CO. However, the presence of any of the catalysts changes the reaction pathway and reduces the energy barrier, indicating that these catalysts promote C6H5CHO decomposition.
Graphical abstract The presence of catalysts changes the reaction pathway and the energy barrier decreases in the order Ea (no catalyst)> Ea (CaO)> Ea (γ-Al2O3)> Ea (ZnO), indicating that these catalysts promote C6H5CHO decomposition.
The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C40H20, C80H20, and C140H20) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21G level, and in some cases at the B3LYP/6-31G* level, and the energy associated with the attachment of the OH substituent was determined. The OH-group attachment energy was compared with the OH functionalization of phenanthrene and picene models and with previous results for zigzag (9.0) SWCNT systems. In comparison to zigzag SWCNTs, the armchair form is more (by about 5 to 10 kcal mol?1) reactive toward hydroxylation.
Figure The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C40H20, C80H20, and C140H20) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21 G level, and in some cases at the B3LYP/6-31 G* level, and the energy associated with the attachment of the OH substituent was determined.
Second group metal dimers can replace the carbon atom in benzene to form metallabenzene (C5H6M2) compounds. These complexes possess some aromatic character and promising hydrogen adsorption properties. In this study, we investigated the aromatic character of these compounds using aromaticity indices and molecular orbital analysis. To determine the nature of interactions between hydrogen and the metallic center, variation-perturbational decomposition of interaction energy was applied together with ETS-NOCV analysis. The results obtained suggest that the aromatic character comes from three π orbitals located mainly on the C5H5? fragment. The high hydrogen adsorption energy (up to 6.5 kcal mol?1) results from two types of interaction. In C5H6Be2, adsorption is controlled by interactions between the empty metal orbital and the σ orbital of the hydrogen molecule (Kubas interaction) together with corresponding back-donation interactions. Other C5H6M2 compounds adsorb H2 due to Kubas interactions enhanced by H2–π interactions.
Spin–spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob’s ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict 1JOH, 2JHH and 2hJOO couplings, while 1hJOH is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for 1JOH and 2JHH have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods.
Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C6(CH3)62+, in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C7H7)3+, in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C8H8 compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage.
Graphical abstract Possible structural transformations of stable configurations of (C7H7)3+, which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.
A systematic study on the first excited-state proton transfer (ESPT) in 2RAI-H2O (R = OH, OCH3, CN, NO2, CHO) complexes in solution were investigated at the TD-M06-2X/6-31 + G(d, p) level. The double proton transfer occurred in an asynchronous but concerted protolysis fashion no matter which substituent R was used at C2 position in pyrrole ring in the 7AI-H2O complex. The specific vibrational-mode of ESPT in the model systems was confirmed and contributed to promote the reaction rate by shortening the reaction path. The substituent effects of different groups on the ESPT thermodynamics and kinetics were discussed. It was obvious that the geometries, barrier height, asynchrony, and specific vibration-mode of excited-state proton transfer changed with the different substituent groups.
Graphical Abstract The distance between two neighboring heavy atoms such as N1-O11 (R1) and O11-N8 (R2) distances played an important role in the proton transfer reaction. The sum of the N1-O11 and O11-N8 distances in the reactant of 2RAI-H2O (R=H, OH, OCH3; CN, CHO, NO2) complexes is in the range of 5.542 Å~5.692 Å and changes along with the substituent group at C2 position in the pyrrole ring. The ESDPT barrier height and the sum of the N1-O11 and O11-N8 distances have a good correlation.
Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n?=?6–9 and k?=?2–4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (Lt) and the diameter (dt) of the pristine CNT has to be larger than 2, i.e., Lt/dt?>?2, in order to provide the observed experimental trends of C=C bond distances, as well as to maintain the atomic charges nearly constant and zero around the center of the tube. Therefore, the concepts of useful length and volume were developed and tested for the encapsulation process of HCN and C2H2 into CNTs. The energies involved in these processes, as well as the changes in molecular structure and electronic properties of the dopants and the CNTs are discussed and rationalized by the amount of charge transferred between dopant and CNT.
The capacity of SX2 (X = F, Cl, and Br) to engage in different kinds of noncovalent bonds was investigated by ab initio calculations. SCl2 (SBr2) has two σ-holes upon extension of Cl (Br)?S bonds, and two σ-holes upon extension of S?Cl (Br) bonds. SF2 contains only two σ-holes upon extension of the F?S bond. Consequently, SCl2 and SBr2 form chalcogen and halogen bonds with the electron donor H2CO while SF2 forms only a chalcogen bond, i.e., no F···O halogen bond was found in the SF2:H2CO complex. The S···O chalcogen bond between SF2 and H2CO is the strongest, while the strongest halogen bond is Br···O between SBr2 and H2CO. The nature of these two types of noncovalent interaction was probed by a variety of methods, including molecular electrostatic potentials, QTAIM, energy decomposition, and electron density shift maps. Termolecular complexes X2S···H2CO···SX′2 (X = F, Cl, Br, and X′ = Cl, Br) were constructed to study the interplay between chalcogen bonds and halogen bonds. All these complexes contained S···O and Cl (Br)···O bonds, with longer intermolecular distances, smaller values of electron density, and more positive three-body interaction energies, indicating negative cooperativity between the chalcogen bond and the halogen bond. In addition, for all complexes studied, interactions involving chalcogen bonds were more favorable than those involving halogen bonds.
Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C60 fullerene (i.e., C30), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titanium atom on C30 occurs in the concave surface of the molecule. Afterward, we investigated the interaction of the system C30-titanium with carbon monoxide and carbon dioxide molecules, respectively. We found that each of these molecules is chemisorbed, with no dissociation. The value of the adsorption energy for the carbon monoxide molecule varies from ?0.897 to ?1.673 eV, and for the carbon dioxide molecule, it is between ?1.065 and ?1.274 eV. These values depend on the initial orientation of these molecules with respect to TiC30.
Magnetic shielding constants for an isolated fullerene C60, cucurbituril CB[9], and the host-guest complex C60@CB[9] were calculated as a function of separation of the monomers. Our results in the gas phase and water indicate a significant variation of the magnetic properties for all atoms of the monomers in the complex and after liberation of fullerene C60 from the interior of the CB[9] cavity. The interaction between the two monomers results in a charge transfer that collaborates with a redistribution of electron density to deshield the monomers.
The dual role of the ionic liquid 1-butyl-3-methyl-imidazolium trifluoroacetic acid ([C4mim]TFA) as an extractant for thiophene (TH) and a catalyst for the oxidation of TH was explored at the molecular level by performing density functional theory (DFT) calculations. The calculated interaction energies demonstrated why [C4mim]TFA is a better extractant for thiophene sulfone (THO2) than for TH. Two pathways were proposed for the oxidation of TH to THO2 with [C4mim]TFA acting as a catalyst. In the dominant pathway, a peracid is formed which then oxidizes TH to the sulfoxide and sulfones. The presence of [C4mim]TFA was found to greatly reduce the barrier to the oxidative desulfurization (ODS) of TH using H2O2 as an oxidant.
The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 and C82 fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C2 corrections were included in the calculation of fragmentation energies for comparison with experimental C2 fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C2 fragmentation of C80, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{80}}}} ^{ + } } \right)}\) agree well with experimental data, whereas in the case of C82 fragmentation, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{82}}}} ^{ + } } \right)}\) exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C2 fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.
Figure C2 fragmentation energies of C80 and C82 fullerenes have been calculated with B3LYP/6-31G* model chemistry, with semiempirical self-consistent-charge density-functional tight-binding (SCC-DFTB) method and with the more rigorous MP2 method. The influence of basis set extension and level of theory on the resulting fragmentation energies is discussed
Human matrix metalloproteinase (MMP)-1 or collagenase–1 plays a significant role in embryonic development, tissue remodeling, and is also involved in several diseases like arthritis, metastasis, etc. Molecular dynamics simulation studies on hMMP-1 X-ray structures (PDB Id. 1CGE, 1CGF, 1CGL, 1HFC, and 2TCL) suggest that the three conserved water molecules (WH/1, WI, WS) are coordinated with catalytic zinc (ZnC), and one water molecule (W) is associated at structural zinc ion (ZnS). Transition of the coordination geometry around ZnC from tetrahedral to octahedral and tetrahedral to trigonal bipyramidal at ZnS are also observed during the dynamics. Recognition of two zinc ions through water mediated bridges (ZnC – WH (W1)…W2….H183 – ZnS) and stabilization of secondary coordination zone around the metal ions indicates the possibility of ZnC…ZnS coupled catalytic mechanism in hMMP-I. This study not only reveals a functionally important role of conserved water molecules in hMMP-I but also highlights the involvement of other non catalytic residues, such as S172 and D170 in the catalytic mechanism. The results obtained in this study could be relevant for importance of conserved water mediated recognition site of the sequence residue id. 202(RWTNNFREY)210, interaction of W(tryptophan)203 to zinc bound histidine, their influence on the water molecules that are involved in bridging between ZnC and ZnS, and structure-based design of specific hMMP inhibitors.
We report first-principles calculations carried out to analyze the adsorption of calcium on the outer surface of the fullerene C60, yielding [C60?+?mCa]. Geometric optimization (GO) and molecular dynamics (MD) simulation were performed using the plane-wave pseudopotential method within the framework of density functional theory (DFT) and time-dependent DFT (TD-DFT) to investigate the configurations, the associated energies in the ground state, and the stabilities of fullerenes and endofullerenes doped with radioactive sodium iodide when they interact with calcium atoms on the outer fullerene surface (i.e., [nNa131I@C60?+?mCa]). The reason for investigating these calcium-functionalized (endo)fullerene systems was to gauge their potential stability when used as vectors to deliver radioiodine to cancerous tissue in the human body. In the simulations, we found that the geometric limit on the number of calcium atoms that can be physisorbed on the outer surface of an empty fullerene while maintaining its structural stability is 28 calcium atoms, which also takes into account the proportional expansion of the fullerene as the number of absorbed calcium atoms increases. However, the stability of a fullerene system during calcium adsorption also strongly depends on whether any atoms or molecules are being encapsulated by the fullerene, as these encapsulated atoms/molecules can also interact with the fullerene and influence its stability. A Mulliken electronegativity analysis revealed that, when atoms inside and/or outside the fullerene donate charge (electrons) to the fullerene, the fullerene expands. The excess charge on the carbon atoms of the fullerene weakens some of the carbon–carbon bonds, potentially causing them to break, in which case the fullerene loses its ability to encapsulate molecules and releases them.
Graphical Abstract DFT simulation of a endo fullerene doped with radioactive sodium iodide interacting with 28 calcium atoms in a geometric arrangement
The effect of alkali metal oxides MnO (M?=?Li, Na, K; n?=?2, 3, 4) on the geometric, electronic, and linear and nonlinear optical properties of the Mg12O12 nanocage was investigated by density-functional-based methods. According to the computational results, these alkali metal oxides are adsorbed on the Mg12O12 nanocage because this adsorption reduces its energy gap. The static first hyperpolarizability (β0) of the nanocage is dramatically increased in the presence of the alkali metal oxides, with the greatest increase seen in the presence of the superalkalis (i.e., M3O; M?=?Li, Na, and K). The highest first hyperpolarizability (β0?≈?600,000 a.u.) was calculated for K3O@Mg12O12, which was considerably more than that for Mg12O12. The thermodynamic properties and relative stabilities of these inorganic compounds are discussed.
Utilizing first-principles calculations, we studied the electronic and optical properties of C24, C12X6Y6, and X12Y12 fullerenes (X?=?B, Al; Y?=?N, P). These fullerenes are energetically stable, as demonstrated by their negative cohesive energies. The energy gap of C24 may be tuned by doping, and the B12N12 fullerene was found to have the largest energy gap. All of the fullerenes had finite optical gaps, suggesting that they are optical semiconductors, and they strongly absorb UV radiation, so they could be used in UV light protection devices. They could also be used in solar cells and LEDs due to their low reflectivities.
The nucleation, ice crystal shapes and thermodynamic stability of polar stratospheric clouds particles are interesting concerns owing to their implication in the ozone layer destruction. Some of these particles are formed by conformers of H2O, HNO3, and H2SO4. We carried out calculations using density functional theory (DFT) to obtain optimized structures. Several stable trimers are achieved —divided in two groups, one with HNO3 moiety, second with H2SO4 moiety— after pre-optimization at B3LYP/6-31G and subsequently optimization at B3LYP/aug-cc-pVTZ level of theory. For both most stable conformers five H2O molecules are added to their optimized trimers to calculate hydrated geometries. The OH stretching harmonic frequencies are provided for all aggregates. The zero-point energy correction (ZEPC), relative electronic energies (?E), relative reaction Gibbs free energies ?(?G)k-relative, and cooling constant (Kcooling) are reported at three temperatures: 188 K, 195 K, and 210 K. Shapes given in our calculations are compared with various experimental shapes as well as comparisons with their thermo-stabilities.
Graphical Abstract Facet shapes and thermo-stabilities of H2SO4?HNO3 hydrates involved in polar stratospheric clouds. IR spectrum of WNS-1+5W structure and its circular facet
The cooperativity effects of the H-bonding interactions in HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane)???HMX???FA (formamide), HMX???HMX???H2O and HMX???HMX???HMX complexes involving the chair and chair–chair HMX are investigated by using the ONIOM2 (CAM-B3LYP/6–31++G(d,p):PM3) and ONIOM2 (M06-2X/6–31++G(d,p):PM3) methods. The solvent effect of FA or H2O on the cooperativity effect in HMX???HMX???HMX are evaluated by the integral equation formalism polarized continuum model. The results show that the cooperativity and anti-cooperativity effects are not notable in all the systems. Although the effect of solvation on the binding energy of ternary system HMX???HMX???HMX is not large, that on the cooperativity of H-bonds is notable, which leads to the mutually strengthened H-bonding interaction in solution. This is perhaps the reason for the formation of different conformation of HMX in different solvent. Surface electrostatic potential and reduced density gradient are used to reveal the nature of the solvent effect on cooperativity effect in HMX???HMX???HMX.
The character of the bridged hydrogen atom (Hb) of B2H6 has become a hot issue in recent years. In this work, the complexes B2H6?·?·?·?NH3, B2H2X4?·?·?·?nNH3 (n?=?1, 2) and 2HF?·?·?·?B2H2X4?·?·?·?2NH3 (X?=?Cl, Br, I) were constructed and studied based on the M06-2X calculations to investigate how to enhance the Hb?·?·?·?N hydrogen-bonded interaction. When the terminal hydrogen atoms (Ht) of B2H6 were replaced by X (X?=?Cl, Br, I) atoms, the Hb?·?·?·?N hydrogen bond were strengthened. According to the electrostatic potentials in B2H2X4, two HF molecules were added to the interspace of the B-H-B-H four-membered ring of the B2H2X4?·?·?·?2NH3 complexes, and H?·?·?·?X hydrogen bond formed, resulting in further enhancing effect of Hb?·?·?·?N hydrogen bond. As a result, the positive cooperative effect of Hb?·?·?·?N hydrogen bond and H?·?·?·?X hydrogen bond do enhance the interactions of each other. The two measures not only enhance the strength of Hb?·?·?·?N hydrogen bond, but also achieve the goal to make the Hb?·?·?·?N hydrogen bond perpendicular to B?·?·?·?B direction.
This paper inquires the C60 capabilities to contain radio-iodide (131I2) molecules. The encapsulation conditions are investigated applying first principles method to simulate with geometric optimizations and molecular dynamics at 310 K and atmospheric pressure. We find that the n131I2@C60 system, where n?=?1, 2, 3…, is stable if the content does not exceed three molecules of radio-iodide. The application of density functional theory allows us to determine that, the nanocapsules content limit is related with the amount of charge that is transferred from the iodine 131I2 molecules to the carbon atoms in the fullerene surface. The Mulliken population analysis reveals that the excess of charge increases the repulsive forces between atoms and the bond length average in the C60 structure. The weakened bonds easily break and will critically damage the encapsulation properties. Additionally, we test the interaction nanocapsules with different amounts of radioactive iodine diatomic molecules content with calcium atoms, and find that only the fullerene containing one radioactive iodine diatomic molecule was able to interact with up to nine atoms of calcium without disrupting or cracking. Other fullerenes with two and three radio iodine diatomic molecules cannot resist the interaction with a single calcium atom without cracking or being broken.
