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Showing papers in "Structural Chemistry in 2014"


Journal ArticleDOI
TL;DR: In this article, the electronic properties of the benzo[a]pyrene diol epoxide enantiomers, along with a detailed analysis of the energy landscape, geometry, and electronic configuration of the epoxide ring, were analyzed.
Abstract: Benzo[a]pyrene is a known carcinogen, which derives from fossil fuel combustion, cigarette smoke, and generic biomass combustion including traffic emissions. This potent carcinogen has a well-known mechanism of action, leading to the formation of adducts with the DNA, primarily at guanosine positions. The reactivity and chemistry of this notorious compound are, however, dependent on the electronic configuration of the biologically activated metabolite, the benzo[a]pyrene diol epoxide. The activated metabolite exists mainly as four isomers, which have particular chemical reactivities toward guanosine sites on the DNA. These isomers exert also a different carcinogenicity compared to one another, which is a feature that is conventionally attributed to their geometry. However, the reactivity and properties of the isomers are not fully defined, and a determination of these properties by wavefunction behavior is required. This study reports the electronic properties of the benzo[a]pyrene diol epoxide enantiomers, along with a detailed analysis of the energy landscape, geometry, and electronic configuration of the epoxide ring. The results show that the epoxide ring, the core of the reactivity, bears different properties at the level of wavefunction for each isomer. Each of the isomers has a distinct profile on the epoxide ring, in terms of hydrogen bonds and in terms of the non-covalent interaction between the diol groups and the epoxide. These profiles generate differential reactivities of epoxide group, which can be attributed to its local bond lengths, the electron localization function, and polarized bonds. Most interestingly, the quantum chemical calculations showed also that the epoxide ring is inclined more perpendicularly toward the angular ring plane for the more carcinogenic isomers, a feature which suggests a potential geometrical relationship between the inclination of the epoxide group and its interaction with the guanosine group upon adduct formation. Our results introduce novel and crucial information, which assist in understanding the mechanism of toxic potential of this known molecule, and display the strength and level of detail of applying quantum chemical methods to reveal the reactivity, energy properties, and electronic properties of a mutagen.

286 citations


Journal ArticleDOI
TL;DR: In this article, the authors reported the electronic properties of graphyne and its related structures (graphdiyne, graphyne-3, graphyny-4) based on first principle calculation using generalized gradient approximation.
Abstract: Based on first principle calculation using generalized gradient approximation, we report electronic properties of graphyne and its related structures (graphdiyne, graphyne-3, graphyne-4). Boron and nitrogen atoms are systematically substituted into the position of carbon atom and the corresponding changes of the properties are reported. All the structures are found to be direct band gap semiconductors with band gap depending on the concentration and position of the doping material. Our band structure calculation clearly shows that the band gap can be tuned by B–N doping and the spin-polarized calculation depicts the nonmagnetic nature of these structures. The possibility of modulating the band gap provides flexibility for its use in nanoelectronic devices. Projected density of state (PDOS) analysis shed insights on the bonding nature of these novel materials, whereas from the view point of Crystal Orbital Hamilton Population (–COHP) analysis, the nature of chemical bonding between neighbouring atoms and the orbital participating in bonding and antibonding have been explored in details.

83 citations


Journal ArticleDOI
TL;DR: In this paper, HCN adsorption on pristine and Si-doped graphynes was studied using density-functional calculations in terms of geometric, energetic, and electronic properties, and it was found that HCN molecule is weakly adsorbed on the pristine graphyne and slightly affects its electronic properties.
Abstract: Graphyne, a lattice of benzene rings connected by acetylene bonds, is one-atom-thick planar sheet of sp- and sp2-bonded carbons differing from the hybridization of graphene (considered as pure sp2). Here, HCN adsorption on the pristine and Si-doped graphynes was studied using density-functional calculations in terms of geometric, energetic, and electronic properties. It was found that HCN molecule is weakly adsorbed on the pristine graphyne and slightly affects its electronic properties. While, Si-doped graphyne shows high reactivity toward HCN, and, in the most favorable state, the calculated adsorption energy is about −10.1 kcal/mol. The graphyne, in which sp-carbon was substituted by Si atom, is more favorable for HCN adsorption in comparison with sp2-carbon. It was shown that the electronic properties of Si-doped graphyne are strongly sensitive to the presence of HCN molecule and therefore it may be used in sensor devices.

70 citations


Journal ArticleDOI
TL;DR: In this article, the authors investigated the cooperativity between the S···N(C) bond and the hydrogen/lithium/halogen bond interactions in O2S···NCX·NCH and O2s···CNX···CNH triads (X=H, Li, Cl, and Br).
Abstract: Ab initio calculations were performed to investigate the cooperativity between the S···N(C) bond and the hydrogen/lithium/halogen bond interactions in O2S···NCX···NCH and O2S···CNX···CNH triads (X=H, Li, Cl, and Br). To understand the properties of the systems better, the corresponding dyads are also studied. It is evident that the lithium bond has a bigger influence on the chalcogen bond than vice versa. The results indicate that the enhanced interaction energies of the S···N(C) and X···N(C) interactions in the triad increase in the order NCCl < NCBr < NCH < NCLi and CNCl < CNBr < CNH < CNLi. This is the order of the increasing positive electrostatic potential V S,max on the X atom. The nature of S···N(C) and X···N(C) interactions of the complexes is unveiled by energy decomposition analysis and natural bond orbital (NBO) theory. The cooperativity between both types of interaction is chiefly caused by the electrostatic effects.

50 citations


Journal ArticleDOI
TL;DR: In this article, the authors used the CCSD(T)/aug-cc-pVTZ/BH&HLYP/aug-CC-pVDZ method to characterize the necessary potential energy surface along the minimum energy path.
Abstract: Thermal rate constants of the CH4 + O2 = CH3 + HO2 reaction were calculated from first principles using both the conventional transition state theory (TST) and canonical variational TST methods with correction from the explicit hindered rotation treatment. The CCSD(T)/aug-cc-pVTZ//BH&HLYP/aug-cc-pVDZ method was used to characterize the necessary potential energy surface along the minimum energy path. We found that the correction for hindered rotation treatment, as well as the re-crossing effects noticeably affect the rate constants of the title process. The calculated rate constants for both forward and reverse directions are expressed in the modified Arrhenius form as $$k_{\text{forward}}^{\text{CVT/HR}} = 2.157 \times 10^{ - 18} \times T^{2.412} \times \,\exp \,( - \frac{25812}{T})$$ and $$k_{\text{reverse}}^{\text{CVT/HR}} = 1.375 \times 10^{ - 19} \times T^{2.183} \times \,{\kern 1pt} \exp \,\,(\frac{2032}{T})$$ (cm3 molecule−1 s−1) for the temperature range of 300–2,500 K. Being in good agreement with literature data, the results provide solid basis information for the investigation of the entire alkane + O2 = alkyl radical + HO2 reaction class.

49 citations


Journal ArticleDOI
TL;DR: In this paper, the adsorption of CO onto Pddecorated (5,5) single-walled carbon nanotube (Pd/SWCNT) and Pd-doped (5 5) singlewalled CNT-V was investigated using ab initio studies.
Abstract: In this paper, the adsorption of CO onto Pd-decorated (5,5) single-walled carbon nanotube (Pd/SWCNT) and Pd-doped (5,5) single-walled carbon nanotube (Pd/SWCNT-V) has been investigated using ab initio studies. The larger binding energies and charges transfer show that the adsorption of CO onto Pd/SWCNT is more stable than that of CO onto Pd/SWCNT-V. The Pd/SWCNT can be utilized as good sensors for CO molecules due to strong binding energy and large electron charge transfer between the Pd/SWCNT and this molecule. Furthermore, the topological properties of the electron density distributions for intramolecular interactions have been analyzed in terms of the Bader theory of atoms in molecules. Finally, the natural population analysis method has been used to evaluate the Pd–C and Pd/CO interactions.

42 citations


Journal ArticleDOI
TL;DR: In this paper, first-principles calculations including dispersion correction are carried out to investigate pristine and Na-decorated graphene-like BC3 (h-BC3) for their application as methane storage materials.
Abstract: First-principles calculations including dispersion correction are carried out to investigate pristine and Na-decorated graphene-like BC3 (h-BC3) for their application as methane storage materials. Structural optimization shows that the methane is physisorbed on the pristine sheet via van der Waals forces with adsorption energy of −2.7 kcal/mol. It was found that unlike the pristine graphene, sodium decorated sheet can effectively interact with the CH4 molecule, so that each metal atom bound on sheet may adsorb up to four CH4. Furthermore, no bond dissociation was observed for the adsorption of CH4 on Na-decorated h-BC3, which means that decorated sheet can act as a storage device for methane safety storage. The results indicate that decoration of the Na atom on surface of sheet induces significant changes in electronic properties of the sheet and its E g is unchanged after adsorption of CH4 molecules. Theoretical methane storage capacity of Na-decorated BC3 nanosheet could approach 18.1 wt%.

38 citations


Journal ArticleDOI
TL;DR: In this paper, the interactions between G, S-doped graphene (SG), and 2S-Doped G (2SG) with eight small molecules including molecular halogens, CH 3OH, CH3SH, H2O, and H2S were studied using density functional theory calculations.
Abstract: Graphene is an important material in adsorption processes because of its high surface. In this work, the interactions between graphene (G), S-doped graphene (SG), and 2S-doped graphene (2SG) with eight small molecules including molecular halogens, CH3OH, CH3SH, H2O, and H2S were studied using density functional theory calculations. The adsorption energies showed that the SG was the best adsorbent, fluorine was the best adsorbate, and all molecular halogens were adsorbed on graphenes better than the other molecules. Most adsorption processes in the gas phase were exothermic with small positive ΔG ads. Moreover, the solvent effect on the adsorption process was examined and all ΔH ads and ΔG ads values for adsorption processes tended to be more negative in all solvents. Therefore, most adsorption processes in the solvents were thermodynamically favorable. The second order perturbation energies obtained from NBO calculations confirmed that the interactions between molecular halogens and our molecules had more strength than those of other molecules. The Laplacian of ρ values obtained from the AIM calculations indicated that the type of interaction in all our complexes was one of closed shell interaction. The MO results and DOS plots also revealed that sulfur doping could increase the conductivity of graphene and this conductivity was enhanced more when they interacted with molecular halogens.

38 citations


Journal ArticleDOI
TL;DR: The results show that the BNNTs can act as a suitable drug delivery vehicle of collagen amino acids within biological systems and are extremely relevant in order to identify the potential applications of functionalized BNN Ts as drug delivery systems.
Abstract: The interaction of collagen amino acids with (5, 5) armchair and (9, 0) zigzag single-walled boron nitride nanotubes (BNNTs) are studied using density functional theory. Our results show that the BNNTs can act as a suitable drug delivery vehicle of collagen amino acids within biological systems. DFT-LDA/DNP calculations revealed that the binding and solvation energies were negative for (5, 5)/(9, 0) BNNTs–collagen amino acid complexes implying the thermodynamic favorability and spontaneous interactions of collagen amino acids with BNNTs sidewall. These results were extremely relevant in order to identify the potential applications of functionalized BNNTs as drug delivery systems.

33 citations


Journal ArticleDOI
TL;DR: In this paper, the authors provide quantitative tools to thoroughly and comprehensively determine antiradical mechanisms of kaempferol in different media, and point to HAT and SPLET mechanisms as operative for all solvents under investigations.
Abstract: Kaempferol, one of the most bioactive plant flavonoids was experimentally and theoretically (at M05-2X/6-311G(d,p) level of theory) investigated for its ability to scavenge potentially, highly damaging hydroxyl and superoxide anion radicals. Relating the obtained hydroxyl radical activity sequence with kaempferol structural features, it could be assumed that C4′-OH functional most probably renders it as hydroxyl radical scavenger, while C5-OH group has more prominent role compared to ortho-hydroxy groups in B ring. However, kaempferol’s activity toward superoxide anion radical implicates ortho-hydroxy groups in B ring as more relevant. Theoretical calculations point to HAT and SPLET mechanisms as operative for kaempferol in all solvents under investigations. The present paper aims to provide quantitative tools to thoroughly and comprehensively determine antiradical mechanisms of kaempferol in different media.

29 citations


Journal ArticleDOI
TL;DR: In this article, the adsorbed energy on the apex of oxygen atom in nanocone was found to be −8.432 eV and the average variation in the energy gap was 50 % for CO adsorption on apex of the oxygen atom.
Abstract: Adsorption properties of CO molecule on NiO nanocone were investigated using density functional approach in terms of adsorbed energy, structural, and electronic properties. The results of the present study reveal that the favorable adsorption site for CO molecule is to the oxygen atom on the apex of NiO nanocone. The adsorbed energy on the apex of oxygen atom in nanocone is found to be −8.432 eV. The average variation in the energy gap is found to be 50 % for CO adsorption on apex of oxygen atom. The Mulliken population analysis and density of states also confirm the adsorption of CO on to the oxygen atom in the apex of nanocone. The present result provides the insight to fine-tune the sensing properties of CO on to the NiO nanocone and enhance the sensing properties.

Journal ArticleDOI
TL;DR: In this paper, a conformational analysis led to ten stable conformers that can be either gauche or anti depending on the dihedral angle values taken by ethylamine side chain and the 5-hydroxyl group.
Abstract: Density functional theoretical studies on hydrogen-bonded complexes of serotonin with methanol/ethanol have been carried out in a systematic way. The conformational analysis led to ten stable conformers that can be either gauche or anti depending on the dihedral angle values taken by ethylamine side chain and the 5-hydroxyl group. Serotonin-molecules strongly bind with ethanol than methanol. Ethylamine side chain is the most reactive site in both methanol/ethanol complexes and it is responsible for the stability order. The topological parameters, electron density, and Laplacian of electron density show excellent correlation with the hydrogen bond length. Natural bond orbital analysis confirms C–H···O hydrogen bond formed between the serotonin–alcohol complexes to be red shift in nature except for Gph(out)anti complex both with methanol and ethanol to be blue shifted. The energy decomposition analysis reveals that strong interactions between serotonin and ethanol/methanol are due to the attractive contributions from the electrostatic component.

Journal ArticleDOI
TL;DR: The linear (multiple linear regressions) and nonlinear (support vector machine) methods are used to develop quantitative structure–activity relationship models in order to predict the activities of some α1β4 integrin inhibitors and indicated the superiority of the genetic algorithm over the stepwise method for feature selection.
Abstract: In this work, the linear (multiple linear regressions) and nonlinear (support vector machine) methods are used to develop quantitative structure–activity relationship models in order to predict the activities of some α1β4 integrin inhibitors. A dataset that consisted of 51 molecules was divided into the training and test subsets. Stepwise and genetic algorithm methods have been employed for selection of relevant descriptors. Comparison of the obtained results indicated the superiority of the genetic algorithm over the stepwise method for feature selection. The models were validated using the cross-validation, external test set, and Y- randomization test. Comparison of the results showed that SVM was very accurate approach in predicting the activities of α1β4 integrin inhibitors. The predicted results of this study can provide better insights to design new α1β4 integrin inhibitors.

Journal ArticleDOI
TL;DR: In this paper, the UB3LYP method was used to investigate the cation-π complexes between several cations (Li, Na+, K+, Be2+, Mg2+, and Ca2+) and different π-systems such as para-substituted (F, Cl, OH, SH, CH3, and NH2) derivatives.
Abstract: Cation–π complexes between several cations (Li+, Na+, K+, Be2+, Mg2+, and Ca2+) and different π-systems such as para-substituted (F, Cl, OH, SH, CH3, and NH2) benzene derivatives have been investigated by UB3LYP method using 6-311++G** basis set in the gas phase and the water solution. The ions have shown cation–π interaction with the aromatic motifs. Vibrational frequencies and physical properties such as dipole moment, chemical potential, and chemical hardness of these compounds have been systematically explored. The natural bond orbital analysis and the Bader’s quantum theory of atoms in molecules are also used to elucidate the interaction characteristics of the investigated complexes. The aromaticity is measured using several well-established indices of aromaticity such as NICS, HOMA, PDI, FLU, and FLUπ. The MEP is given the visual representation of the chemically active sites and comparative reactivity of atoms. Furthermore, the effects of interactions on NMR data have been used to more investigation of the studied compounds.

Journal ArticleDOI
TL;DR: In this article, structural and electronic properties of single wall (5,5) boron nitride nanotubes functionalized on the surface and at the ends with paracetamol (C8H9NO2) have been investigated within the density functional theory as implemented in DMol3 quantum chemistry code.
Abstract: We have investigated structural and electronic properties of single wall (5,5) boron nitride nanotubes functionalized on the surface and at the ends with paracetamol (C8H9NO2). Studies have been done within the density functional theory as implemented in DMol3 quantum chemistry code. The exchange and correlation energies have been treated according to the generalized gradient approximation with the Perdew–Burke–Ernzerhof parameterization and a basis function with double polarization. The geometry optimization of the (5,5) BNNT-Paracetamol system has been done using the criterion of minimum energy considering eight possible atomic interacting configurations. Simulation results show that the preferential interaction (physisorption) site of the paracetamol is on the nanotube surface in a parallel configuration and making an angle of 45° in the perpendicular direction to the nanotube. The BNNT-Paracetamol system experiences an increase in the polarity which favors the possible dispersion and solubility. As a result of the interaction, the functionalized nanotube chemical reactivity is increased. Provided the work function of the nondoped BNNT-Paracetamol structure decreases as compared with the pristine BNNT, the functionalized nanotubes yielded conditions to improve field emission properties consequently, they may be used as biosensors of paracetamol. Finally, the nanotube doped with carbon atoms induces chemisorption and an increase in the polarity, reactivity, and reduction in the work function. Taking into account, these results it may be suggested the use of the system in sensor devices and optoelectronic systems.

Journal ArticleDOI
TL;DR: In this article, a new series of donor-acceptor-donor (D-A-D) type luminescent mesogens carrying 2-methoxy-3-cyanopyridine as a central core linked with variable alkoxy chain lengths (m = 6 and 8) as terminal substituents was synthesized and characterized using spectral methods.
Abstract: A new series of donor-acceptor-donor (D-A-D) type luminescent mesogens carrying 2-methoxy-3-cyanopyridine as a central core linked with variable alkoxy chain lengths (m = 6 and 8) as terminal substituents was synthesized and characterized using spectral methods. The newly synthesized molecules were subjected to single-crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), differential scanning calorimetric (DSC), polarizing optical microscopy (POM), and fluorescence emission studies in order to ascertain their mesogenic and photophysical properties. The SCXRD data on 4a and 4b reveal that the presence of short intermolecular contacts, viz. C-H center dot center dot center dot N, C-H center dot center dot center dot O, C-H center dot center dot center dot pi, and pi center dot center dot center dot pi interactions, is responsible for their crystal packing. The measured torsion angle values indicate that molecules possess distorted non-planar structure. The DSC, POM, and PXRD studies confirm that all the molecules show thermotropic liquid crystalline behaviour and exhibit rectangular columnar phase. Further, their UV-visible and fluorescence spectral studies reveal that the target molecules are luminescent displaying a strong absorption band in the range of 335-340 nm and a blue fluorescence emission band in the range of 395-425 nm (both in solution and film state) with good fluorescence quantum yields (10-49 %).

Journal ArticleDOI
TL;DR: In this paper, 1-Amino-, 1-ethylamino-, and 1-(diethylamino)-anthraquinone were characterized by UV-Vis spectroscopy, acid-base titration, electrochemical methods, and quantum-chemical calculations at the B3LYP/6-31 ++G** level.
Abstract: 1-Amino-, 1-ethylamino-, and 1-(diethylamino)-anthraquinone were characterized by UV–Vis spectroscopy, acid–base titration, electrochemical methods, and quantum-chemical (QM) calculations at the B3LYP/6-31 ++G** level. Acid–base titration and the relative differences between the free energies of the basic and acidic forms of the studied species show that 1-(diethylamino)anthraquinone is the strongest base in an acetonitrile solution. Moreover, the structural differences between the B3LYP-optimized neutral and protonated anthraquinones, notably the presence or the absence of internal hydrogen bonds, account well for the sequence of the measured/calculated basicity. The basicity of the investigated compounds strongly influences their electrochemical properties in acetonitrile. Indeed, the cyclic voltammograms of 1-aminoanthraquinone and 1-(ethylamino)anthraquinone display two well-resolved reduction waves that indicate a two-step reduction process (EE mechanism). On the other hand, the electroreduction of 1-(diethylamino)anthraquinone becomes complicated by the interaction of its reduced forms with traces of water present in an acetonitrile solution (ECE mechanism). The mechanism of this reaction is proposed, and its possibility to occur is examined based on QM calculations.

Journal ArticleDOI
TL;DR: In this article, the structure of benzene-acetylene co-crystal was analyzed based on calculated energies of intermolecular interactions between basic molecules located in asymmetric part of unit cell and their neighbours belonging to their first coordination sphere.
Abstract: Crystal structure of benzene–acetylene co-crystal was analysed based on calculated energies of intermolecular interactions between basic molecules located in asymmetric part of unit cell and their neighbours belonging to their first coordination sphere. It is demonstrated that the basic structural motif of the crystal is represented by infinite chains formed by the hydrogen-bonded benzene and acetylene molecules. Energy of interaction of the basic pair of molecules to neighbours within the chain is 2.2 times higher than the energy of interactions with molecules of any neighbouring chain. This ratio almost does not depend on method of calculation of interaction energy. Also, results of calculations were compared with analysis of topology of electron density distribution in crystal. The possibility to find the basic structural motif of the crystal based on properties of intermolecular bond critical points is demonstrated.

Journal ArticleDOI
TL;DR: In this paper, the authors developed a QSPR model that allows predicting logarithmic values of the organic carbon/water partition coefficient for 1,436 chlorinated and brominated congeners of persistent organic pollutants based on the computationally calculated descriptors.
Abstract: The organic carbon/water partition coefficient (K OC) is one of the most important parameters describing partitioning of chemicals in soil/water system and measuring their relative potential mobility in soils. Because of a large number of possible compounds entering the environment, the experimental measurements of the soil sorption coefficient for all of them are virtually impossible. The alternative methods, such as quantitative structure–property relationship (QSPR techniques) have been applied to predict this important physical/chemical parameter. Most available QSPR models have been based on correlations with the n-octanol/water partition coefficient (K OW), which enforces the requirement to conduct experiments for obtaining the K OW values. In our study, we have developed a QSPR model that allows predicting logarithmic values of the organic carbon/water partition coefficient (log K OC) for 1,436 chlorinated and brominated congeners of persistent organic pollutants based on the computationally calculated descriptors. Appling such approach not only reduces time, cost, and the amount of waste but also allows obtaining more realistic results.

Journal ArticleDOI
TL;DR: In this paper, the adsorption of CO2 molecule in the interior and exterior surfaces of a BeO nanotube was investigated by means of density functional calculations in terms of energetic, electronic, and geometric properties.
Abstract: The adsorption of CO2 molecule in the interior and exterior surfaces of a BeO nanotube was investigated by means of density functional calculations in terms of energetic, electronic, and geometric properties. It was found that the existence of a CO2 inside a (4, 4) armchair tube is more stable than its adsorption on the outside by about 0.13 kcal/mol. The adsorption on the exterior surface is site-selective so that CO2 prefers to attack a Be atom from its one O-head, releasing energy of 14.30 kcal/mol. By increasing the number of adsorbed CO2 molecules, the adsorption energy is decreased. We predicted that the electronic properties and quantum molecular descriptors of the tube cannot be significantly influenced by the adsorption process.

Journal ArticleDOI
TL;DR: In this paper, the hydrogenation of an aluminum nitride nanosheet (h-AlN) with atomic and molecular hydrogen was investigated, and it was found that atomic H prefers to be adsorbed on an N atom rather than Al, releasing energy of 21.1
Abstract: Employing density functional calculations including an empirical dispersion term, we investigated the hydrogenation of an aluminum nitride nanosheet (h-AlN) with atomic and molecular hydrogen. It was found that atomic H prefers to be adsorbed on an N atom rather than Al, releasing energy of 21.1 kcal/mol. The HOMO/LUMO energy gap of the sheet is dramatically reduced from 107.9 to 44.5 kcal/mol, upon the adsorption of one hydrogen atom. The adsorption of atomic H on the h-AlN presents properties which are promising for nanoelectronic applications. The molecular H2 was found to be adsorbed collinearly on an N atom and dissociated to two H atoms on Al–N bond. Calculated barrier and adsorption energies for this dissociation process are about +18.9 and −1.9 kcal/mol. We predict that each nitrogen atom in an AlN sheet can adsorb two hydrogen molecules on opposite sides of the sheet, and thus the gravimetric density for hydrogen storage on AlN sheet is evaluated to be about 8.9 wt%.

Journal ArticleDOI
TL;DR: In this article, an innovative theoretical study of intermolecular properties of standard hydrogen-bonded complexes of H2O···HCF3, NH3··· HCF3 and NH3·HF was presented, where the MP2/6-311++G(d,p) level of theory was applied to determine the optimized geometries by which the structural parameters, electronic properties, and the stretch vibration modes of these systems were examined.
Abstract: An innovative theoretical study of intermolecular properties of standard hydrogen-bonded complexes of H2O···HCF3, NH3···HCF3, H2O···HF, and NH3···HF is presented in this work. Several computational strategies were used, so initially the MP2/6-311++G(d,p) level of theory was applied to determine the optimized geometries by which the structural parameters, electronic properties, and the stretch vibration modes of these systems were examined. By taking into account the infrared spectrum analysis, the frequency shifted either to the red- or blue-region is the principal interpretation upon formation of intermolecular complexes. Due to this, the analysis of the interaction strengths corroborates with these vibration behaviors, and besides, the Natural Bond Orbital calculations revealed systematic changes in the percentage of the s and p orbitals, by which the stretch deformations on the proton donors (HF and HCF3) could be understood. In advance, it was quoted the appearing of intermolecular covalence in these complexes, and this event could be theoretically discovered through the topological computations based on the Bader's Quantum Theory of Atoms in Molecules.

Journal ArticleDOI
TL;DR: In this paper, the authors applied all the different adopted models for assessing the energy of intramolecular hydrogen bond (IMHB) in simple resonance-assisted hydrogen bond systems (the cis enol form of malonaldehyde, thiomalonaldehyde and a variety of halogenated derivatives), and compared them.
Abstract: The energy of intramolecular hydrogen bond (IMHB) is a central subject in chemistry and biochemistry. In contrast with the IMHBs, there is no general accepted procedure to determine the IMHB energy. In the present study, for the first time, we applied all the different adopted models for assessing the energy of IMHB of O–H···O and O–H···S in simple resonance-assisted hydrogen bond systems (the cis enol form of malonaldehyde, thiomalonaldehyde, and a variety of halogenated derivatives), and compared them. The energy of IMHB, by various methods such as related rotamers method (RRM), rotational barrier method (RBM), conformational analysis method (CAM), isodesmic reaction method (IRM), and open–close method (OCM), was estimated. Exploring and comparing the correlations between the IMHB energies with various descriptors of hydrogen bond strength, such as geometrical, topological, molecular orbital, and spectroscopic parameters, were carried out. According to the theoretical results, we found that both RRM and RBM have the best linear correlations with all of the hydrogen bond descriptors (R ≥ 0.90) while the results of other methods (CAM, IRM and OCM) are not suitable (R ≤ 0.80). Surprisingly, we found that the OCM, which has been widely applied in the estimation of the IMHB energy, has the weakest linear dependent with all of the HB descriptors. Consequently, according to the regression coefficients, the order of linearity of these methods is as follows: RRM > RBM > > CAM > IRM > OCM.

Journal ArticleDOI
TL;DR: In this article, the authors reported the synthesis of three metal (Ni2+, Cu2+, and Zn2+) complexes of N-acetyl-l-cysteine (NAC) using a solvent-free solid-state method.
Abstract: In recent years, interactions of metal ions with amino acid derivatives have been studied extensively due to their immense importance in the life-supporting processes. Here, we report the synthesis of three metal (Ni2+, Cu2+, and Zn2+) complexes of N-acetyl-l-cysteine (NAC) using a solvent-free solid-state method. Characterization of the complexes by elemental analyses, molar conductance, SEM, infrared and electronic absorption spectra reveals that the metal ions bind to the NAC molecules in 1:2 molar ratio (metal:ligand) via the S-atoms. Theoretical calculations are carried out using the B3LYP hybrid functional in combination with 6-31++G(d,p) and LANL2DZ basis sets to investigate the effects of metal coordination on the backbone structural features of NAC and geometry about the α-carbon atom. The molecular geometries of NAC as well as its metal complexes are fully optimized in gas phase without applying any geometrical constraint, and a second derivative analysis confirms that all the optimized geometries are true minima. TD-DFT single-point calculations are performed in aqueous phase to obtain the theoretical λ max values. The gas-phase interaction enthalpies (metal ion binding affinities), Gibbs energies, HOMO/LUMO energies as well as their energy gaps, rotational constants, dipole moments, and theoretically predicted vibrational spectra of all the reaction species are also calculated and thoroughly analyzed. Most of the experimental results are well reproduced by the B3LYP level of calculations. Metal ion coordination to NAC modifies its backbone structural features as well as the geometry about the α-carbon atom.

Journal ArticleDOI
TL;DR: In this paper, the structural and opto-electronic properties of cyclopenta[2,1-b:3,4-b′]dithiophene derivatives have been investigated.
Abstract: Density functional theory calculations were carried out to investigate the structural and opto-electronic properties of cyclopenta[2,1-b:3,4-b′]dithiophene (CPDT) derivatives. The ground state, cationic and anionic geometries of cyclopentadithiophene derivatives were optimized at B3LYP/6-311G(d,p) level of theory. Based on these geometries, ionic state properties such as ionization potentials, electron affinities, hole extraction potential, and electron extraction potential of cyclopentadithiophene derivatives have been calculated. The charge transfer integral, spatial overlap integral, and site energy were calculated from the matrix elements of Kohn–Sham Hamiltonian. Computed results show that the mobility of charge carriers in CPDT derivatives is strongly affected by the substitution of electron withdrawing group at bridge-head and α-positions. The excited state geometry of CPDT derivatives were optimized using configuration interaction singles method. On the basis of ground and excited states geometry, absorption and emission spectra of cyclopentadithiophene derivatives were calculated using the time-dependent density functional theory method. It has been observed that the substitution of EWG in cyclopentadithiophene core alters the absorption and emission spectra. The nonlinear optical property of CPDT derivatives have been studied through computed static polarizability and first hyperpolarizability.

Journal ArticleDOI
TL;DR: In this paper, the authors investigated geometry, strength, and origin of the interactions in linear (FCN)2−7 and (FNC)2-7 clusters by means of MP2 and CCSD(T) methods.
Abstract: A theoretical investigation was performed to study cooperative effects in fluorine-centered halogen bond interactions. We investigated geometry, strength, and origin of the interactions in linear (FCN)2–7 and (FNC)2–7 clusters by means of MP2 and CCSD(T) methods. Our results strongly suggest that cooperative effects induced by fluorine-centered halogen bonds are significant in both linear FCN and FNC clusters. CCSD(T)/6-311++G** calculations reveal that for (FCN)2–7 clusters, the average halogen-bonding energy per monomer increases from −0.76 kcal/mol in dimer to −0.92 kcal/mol in heptamer. The results of electron density analysis suggest that the capacity of the linear FCN and FNC clusters to concentrate electrons at the F···N and F···C BCPs enhance considerably with cluster size. The results also indicate that the magnitude of cooperative effects is more important for FCN than for FNC clusters. According to energy decomposition analysis, attractive electrostatic and dispersion components make the major contribution to the F···N and F···C halogen bond interactions. An acceptable correlation is found between different energy terms and total interaction energies, revealing the main role of these interactions for stability of linear (FCN) n and (FNC) n clusters.

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TL;DR: In this paper, gas phase electron diffraction (GED)-MS and theoretically (DFT and MP2) was used to study the conformational behavior of the title compound 1 and showed that only two conformers of 1 differing by axial or equatorial location of the phenyl group and the angle of rotation about the Si-CPh bond contribute to the equilibrium.
Abstract: Molecular structure and conformational behavior of the title compound 1 were studied experimentally by gas-phase electron diffraction (GED–MS) and theoretically (DFT and MP2). Only two of four possible conformers of 1 differing by axial or equatorial location of the phenyl group and the angle of rotation about the Si–CPh bond contribute to the equilibrium; these are the 1-eq conformer with the phenyl ring plane perpendicular to the averaged silacyclohexane plane and the 1-ax conformer with the phenyl ring and Si–C6 bond lying approximately in one plane. The ratio 1-eq:1-ax is 62 (10):38 (10), which is only slightly different from 78:22 in solution. The presence of up to 10 % of 1-ax_orth conformer cannot be excluded either. The corresponding ΔG values are 0.29 and 0.25 kcal mol−1. The GED molecular structure of 1 is nicely reproduced by DFT and MP2 calculations. .

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TL;DR: In this article, the influence of electric field on the electronic properties of bilayer and trilayer graphyne has been studied using the density functional theory, and it is found that applying a uniform electric field perpendicular to the graphyne sheet changes the electronic property of AB-stacked bilayers and ABC-stacking trilayers so that they become semiconductor.
Abstract: The influence of electric field on the electronic properties of bilayer and trilayer graphyne has been studied using the density functional theory. We have investigated alpha graphyne due to its analogous to graphene. The bilayer and trilayer graphyne with different stacking style configurations have been considered. Our results indicate that the electronic properties of alpha graphyne are insensitive to the number of graphyne layer and configuration. The bilayer and trilayer graphyne are semimetal similar to the monolayer graphyne. It is found that applying a uniform electric field perpendicular to the graphyne sheet changes the electronic properties of AB-stacked bilayer and ABC-stacked trilayer graphyne so that they become semiconductor. The band gaps of the bilayer and trilayer graphyne with these configurations are enhanced by increasing strength of the electric field. Therefore, possibility of controlling the electronic properties of graphyne by applying electric field makes graphyne as a good candidate for next generation nanoelectronic devices.

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TL;DR: In this paper, the B3LYP exchange correlation function with LanL2DZ as basis set was used to obtain structural stability and various parameters such as dipole moment, HOMO-LUMO gap, ionization potential, electron affinity, stability factor, binding energy, vibrational studies and optical absorption were studied and reported.
Abstract: Fluorine substituted cadmium oxide (Cd n O n−1F) cluster for n = 2–6 of linear, ring and three dimensional structures were studied using B3LYP exchange correlation function with LanL2DZ as basis set. Different isomers were optimized to obtain structural stability and various parameters such as dipole moment, HOMO–LUMO gap, ionization potential, electron affinity, stability factor, binding energy, vibrational studies and optical absorption were studied and reported. The stability of the cluster depends on the binding energy and vibrational intensity.

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TL;DR: In this paper, MCM-41 and MSU-H mesoporous silicas were successfully functionalized with hydrogen bonds forming organic moieties, which have been proven by elemental analysis.
Abstract: MCM-41 and MSU-H mesoporous silicas were successfully functionalized with hydrogen bonds forming organic moieties, which have been proven by elemental analysis. Both moieties, based on oxygen and nitrogen containing groups, were introduced with high efficiency—the amount of carbon in all cases exceeded 10 % and the elemental ratios suggest binding to the surface through two or three Si–O–Si bonds. Hydrogen peroxide adsorption was conducted in its aqueous solutions and the amount adsorbed was determined using the ferric thiocyanate method. Results are presented as a function of hydrogen peroxide concentration in aqueous solution from 5 to 30 %. Both functionalized silicas show increased adsorption capacity when compared with that of their unfunctionalized analogues. The surface modified with nitrogen-based organic moiety revealed better adsorption properties as well as higher resistance against oxidation. MSU-H silica, due to its larger pore diameter, provides more space to bind hydrogen peroxide molecules and thus was found to have higher adsorption capacity: it adsorbed up to four times more hydrogen peroxide than MCM-41.