Hydrogen-bonding interactions in acetonitrile oligomers using density functional theory method

Hydrogen-bonding interaction in acetonitrile oligomers is studied using density functional theory method. Two types of hydrogen-bonded oligomers are considered viz. cyclic and ladder. Different levels are used to optimize the geometry of acetonitrile monomer and found that at B3LYP/aug-cc-pvtz level the geometrical parameters and vibrational frequencies are in agreement with the experimental determinations. The BSSE corrected total energies of acetonitrile oligomers show that the cyclic structures are more stable than the ladder and the hydrogen bonds in former are stronger than those in the latter. Many-body analysis approach was used to study the nature of interactions between different molecules in these oligomers. It is found that the contribution from many-body energies to the binding energy of a complex is different in cyclic and ladder structures. An increase and decrease in the energy per hydrogen bond with cluster size for the cyclic and ladder structures, respectively, indicates the positive and negative hydrogen-bond cooperativity, respectively.     

A density functional theory study of interaction between formamide and guanine

Hydrogen bonding in complexes formed between formamide and guanine molecules was completely investigated using density functional theory (DFT) at the 6-311++G(d, p) level. For comparison, the HF and MP2 methods were also used. Nine stable cyclic structures stabilized by two hydrogen bonds were found. One of these was a six-membered ring, five were seven-membered rings, and the others were eight-membered rings. The eight-membered ring is preferable to the seven-and six-membered ones as follows from H-bond lengths and interaction energies. The FG4 structure was calculated to be the most stable, and another cyclic structure, FG5, was least stable because of the six-membered ring and the weakest interaction. The infrared spectrum frequencies, intensities, and vibrational frequency shifts are also reported. The text was submitted by the authors in English.     

A density functional theory study of van der Waals interaction in carbon nanotubes

In this article, we investigate the effect of van der Waals force in zigzag carbon nanotubes (CNTs) including single-wall CNT (SWCNT) and double-walled CNT (DWCNT) structures with several interaction configurations. The solid-state density functional theory is employed to calculate the geometric optimization, normal mode frequencies, and IR and Raman spectra with the periodic boundary condition. For SWCNTs, we find that the Raman intensity is not affected by the tube diameter or the electronic structure. The IR absorption, however, increases with the tube diameter. We find that the close metallicity of the electronic structure has a significant impact on the IR simulations. When the van der Waals force is applied outside the CNTs at a distance longer than 3.0, the effect on Raman spectra is minimal but some effects can still be confirmed by IR absorption. When the van der Waals force acts inside the CNTs, the effect on the spectrum can be observed, especially at a distance of 2.8 Å, both IR and Raman can be significantly enhanced in many modes.     

Hydrogen-bonding interaction of 5,6-dihydrouracil with RNA bases: DFT and MP2 studies

5,6-Dihydrouracil (DHU) is a rare pyrimidine base naturally occurring in tRNAs, it differs from the base uracil due to the saturation of the C₅–C₆ bond. This work presents the interaction energies of complexes formation involving DHU bound to the natural RNA bases adenine (A), uracil (U), guanine (G), and cytosine (C). Full geometry optimization has been performed for the studied complexes by B3LYP/6-31+G(d,p) and MP2/6-31+G(d,p) calculations. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. We find that the stability order is DHU:G > DHU:A > DHU:C  DHU:U.     

A density functional theory study on pelargonidin

A complete conformational analysis on the isolated and polarizable continuum model (PCM) modeled aqueous solution cation, quinonoidal, and anion forms of pelargonidin, comprising the diverse tautomers of the latter forms, was carried out at the B3LYP/6-31++G(d,p) level. The results indicate that the most stable conformer of cationic and quinonoidal forms of pelargonidin are completely planar in the gas phase, whereas that of the anionic form is not planar. In contrast, PCM calculations show that the plane of the B ring is slightly rotated with regard to the AC bicycle in the most stable conformer of the cation and quinonoidal form. The most stable conformers of the cation, both in gas phase and aqueous solution, display anti and syn orientations for, respectively, C2-C3-O-H and C6-C5-O-H dihedral angles, whereas syn and anti orientation of hydroxyls at 7 and 4' positions are nearly isoenergetic. The most stable tautomer of quinonoidal pelargonidin is obtained by deprotonating hydroxyl at C5 in gas phase but at C7 according to PCM. Also, the most stable tautomer of the anion is different in gas phase (hydrogens are abstracted from hydroxyls at C5 and C4') and PCM simulation (C3 and C5). Tautomeric equilibria affect substantially the geometries of the AC-B backbone providing bond length variations that basically agree with the predictions of the resonance model. Most of the conformers obtained display an intramolecular hydrogen bond between O3 and H6'. Nevertheless, this interaction is not present in the most stable anions. Ionization potentials and O-H bond dissociation energies computed for the most stable conformers of cation, quinonoidal, and anion forms are consistent with an important antioxidant activity.     

The degenerate properties of modified purine and pyrimidine DNA bases: a density functional study

Density-functional theory was used to study the properties (binding geometries and affinities for the natural DNA bases) of various degenerate nucleobases, which bind without discrimination to the purines or pyrimidines. The data for purine mimics (Z and K) indicates that although stronger binding strengths are calculated for pairs with cytosine compared with thymine, cytosine binds to a less stable tautomer of the nucleobase mimic. Indeed, the energy differences between the binding strengths and the tautomers effectively cancel and thereby provide a possible explanation for the observed degenerate properties of these molecules. Similar trends are found for the pyrimidine mimics (M and P); however, the energy differences do not cancel, even upon inclusion of environmental effects.     

Hybrid density functional theory for pi-stacking interactions: application to benzenes, pyridines, and DNA bases

The suitability of a hybrid density functional to qualitatively reproduce geometric and energetic details of parallel pi-stacked aromatic complexes is presented. The hybrid functional includes an ad hoc mixture of half the exact (HF) exchange with half of the uniform electron gas exchange, plus Lee, Yang, and Parr's expression for correlation energy. This functional, in combination with polarized, diffuse basis sets, gives a binding energy for the parallel-displaced benzene dimer in good agreement with the best available high-level calculations reported in the literature, and qualitatively reproduces the local MP2 potential energy surface of the parallel-displaced benzene dimer. This method was further critically compared to high-level calculations recently reported in the literature for a range of pi-stacked complexes, including monosubstituted benzene-benzene dimers, along with DNA and RNA bases, and generally agrees with MP2 and/or CCSD(T) results to within +/-2 kJ mol(-1). We also show that the resulting BH&H binding energy is closely related to the electron density in the intermolecular region. The net result is that the BH&H functional, presumably due to fortuitous cancellation of errors, provides a pragmatic, computationally efficient quantum mechanical tool for the study of large pi-stacked systems such as DNA.     

A density functional theory study of sulfur poisoning

Density functional theory calculations have been used to investigate the chemisorption of H, S, SH, and H(2)S as well as the hydrogenation reactions S+H and SH+H on a Rh surface with steps, Rh(211), aiming to explain sulfur poisoning effect. In the S hydrogenation from S to H(2)S, the transition state of the first step S+H-->SH is reached when the S moves to the step-bridge and H is on the off-top site. In the second step, SH+H-->H(2)S, the transition state is reached when SH moves to the top site and H is close to another top site nearby. Our results show that it is difficult to hydrogenate S and they poison defects such as steps. In order to address why S is poisoning, hydrogenation of C, N, and O on Rh(211) has also been calculated and has been found that the reverse and forward reactions possess similar barriers in contrast to the S hydrogenation. The physical origin of these differences has been analyzed and discussed.     

Hydrogen-bonding interactions in the binding of loop 1 of fasciculin 2 to Torpedo californica acetylcholinesterase: a density functional theory study

In the present study, the interactions of model complexes at the interface between loop1 of fasciculin 2 (Fas2) and acetylcholinesterase (AChE) are theoretically explored. Three interaction models based upon the crystal structure of the complex of Fas2 with AChE from Torpedo californica (PDB code ) were fully optimized at the B3LYP/6-311G(d,p) level of theory. The atoms-in-molecules (AIM) approach was employed to characterize the corresponding noncovalent hydrogen bonds through the densities and the Laplacians of electron densities at the bond critical points. The total interaction energy of loop 1 (Fas2) with AChE is predicted to be -99.4 kcal/mol. It is concluded that the Fas2 residue Thr8, which contributes more than half of the total binding energy, plays the most important role among the three binding sites. The energy decomposition results through the Kitaura-Morokuma scheme suggest that the electrostatic term is the major component of the entire interaction energy. The positive cooperativity effect revealed in the Thr8(F)-related models was confirmed through the geometry characteristics, AIM results, and the energy decomposition analysis.     

Optoelectronic properties of benzotrithiophene isomers: A density functional theory study

Benzotrithiophene (BTT) isomers were investigated using density functional theory (DFT) and time‐dependent DFT (TD‐DFT) with the aim to explore their structures, linear optical properties, vertical and adiabatic ionization potentials (IP_v and IP_a), electron affinities (EA_v and EA_a), and reorganization energies (λ). The computed bond lengths and bond angles at the B3LYP/6–311+G (d, p) level of theory are in good agreement with experimental crystal structures of the known BTTs. These molecules are planar with zero dihedral angle, making them an ideal backbone for high charge mobility. The UV–visible spectra of BTT isomers are in the range 280–360 nm. All BTT isomers have low hole/electron reorganization energies, which is the main characteristic of good hole/electron transporting materials, and these isomers in turn have potential applications in the field of organic materials.     

Hydrogen-bonding interaction in a complex of amino acid with urea studied by DFT calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine, and leucine) and urea in gas phase have been carried out using density functional theory (DFT) and ab initio methods at the B3LYP/6-311++g** and MP2/6-311++g** theory levels. The structures, binding energy, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution, and bond characteristics of the mentioned complexes were calculated. Urea is a good H-bond donor and an excellent receptor for highly electronegative atoms like O and N, through the formation of two or more hydrogen bonds. The NH₂ and COOH groups of amino acids can form several different types of H-bonds with urea molecular, as well as C^αH and alkyl side chains. The calculated high binding energy also suggests multiple H-bonds formed in one complex. The OH···O contact is the strongest hydrogen bond interaction with H···O separation around 1.65 Å and its relevant angle close to 176°. The closely linear amide H-bonds NH···O and OH···N strongly stabilize the amino acid–urea complex with H···O separation between 1.89 and 2.38 Å. The weaker CH···O/N H-bonds are also discussed as significant interaction in biological systems involving amino acids.     

A density functional theory study of the benzene-water complex

The intermolecular interaction of the benzene-water complex is calculated using real-space pseudopotential density functional theory utilizing a van der Waals density functional. Our results for the intermolecular potential energy surface clearly show a stable configuration with the water molecule standing above or below the benzene with one or both of the H atoms pointing toward the benzene plane, as predicted by previous studies. However, when the water molecule is pulled outside the perimeter of the ring, the configuration of the complex becomes unstable, with the water molecule attaching in a saddle point configuration to the rim of the benzene with its O atom adjacent to a benzene H. We find that this structural change is connected to a change in interaction from H (water)/pi cloud (benzene) to O (water)/H (benzene). We compare our results for the ground-state structure with results from experiments and quantum-chemical calculations.     

Metal catalyzed ethylene epoxidation:A comparative density functional theory study

Ethylene epoxidation on Ag(111), Pt(111), Rh(111) and Mo(100) has been studied by density functional theory (DFT) calculations. The results show that the adsorption energies of possible adsorbed species involved in the ethylene epoxidation increase in the order: Ag相似文献   

A density functional theory study on acetylene-functionalized BN nanotubes

Covalent functionalization of a zigzag boron nitride nanotube (BNNT) with acetylene has been investigated by density functional theory in terms of energetic, geometric, and electronic properties. It has been found that the most stable functionalized BNNT is the one in which the acetylene is diffused into the tube wall so that two heptagonal and two pentagonal rings are formed, releasing energy of 1.54 eV. In addition, the effect of substituting the hydrogen atoms of C₂H₂ by different functional groups including –F, –CH₂F, –CN, and –OCH₃ on the geometric and electronic properties of the BNNT has been investigated. The reaction energies are found to be in the range of ?1.03 to ?3.13 eV so that their relative magnitude order is as follows: C₂F₂ > (OCH₃)₂C₂ > C₂H₂ > (CH₂F)₂C₂ > (CN)₂C₂, suggesting that the functionalization energy is increased by increasing the electron donating character of the functional groups. Overall, chemical modification of BNNT by the studied groups results in little changes in electronic properties of the tube and may be an effective way for the purification of BNNTs.     

Actinium coordination chemistry: A density functional theory study with monodentate and bidentate ligands

In the current study, the coordination chemistry of nine-coordinate Ac(III) complexes with 35 monodentate and bidentate ligands was investigated using density functional theory (DFT) in terms of their geometries, charges, reaction energies, and bonding interactions. The energy decomposition analysis with naturals orbitals for chemical valence (EDA-NOCV) and the quantum theory of atoms in molecules (QTAIM) were employed as analysis methods. Trivalent Ac exhibits the highest affinities toward hard acids (such as charged oxophilic donors, fluoride), so its classification as a hard acid is justified. Natural population analysis quantified the involvement of 5f orbitals on Ac to be about 30% of total valence electron natural configuration indicating that Ac is a member of the actinide series. Pearson correlation coefficients were used to study the pairwise correlations among the bond lengths, ΔG reaction energies, charges on Ac and donor atoms, and data from EDA-NOCV and QTAIM. Strong correlations and anticorrelations were found between Voronoi charges on donor atoms with ΔG, EDA-NOCV interaction energies and QTAIM bond critical point densities.     

A density functional theory study of copper-catalyzed aziridination of olefins

Density functional theory calculations are reported for the reaction mechanism of selected XCuNHX(X = Cl, Br, I) with olefins to form three-membered ring products. The copper reagents react with olefins via an asynchronous attack on one CH₂ group of ethylene with a relatively low barrier (<78 kJ/mol). These computational results are in good agreement with experimental results, and this suggests that the nitrene transfer process is favored. The BrCuNHBr is found to be the most reactive reagent in the XCuNHX (X = Cl, Br, I) series of reagents. These results are qualitatively consistent with the agreement between copper-catalyzed species character and experimental conditions needed for efficient reaction.     

Thermodynamic and kinetic study of ibuprofen with hydroxyl radical: A density functional theory approach

Ibuprofen, a frequently detected pharmaceutical in natural and engineered waters, was studied in both neutral and anionic forms using density functional theory at the B3LYP/6‐311++G**//B3LYP/6‐31G* level of theory in its reaction with hydroxyl radical ( ? OH). The reaction pathways included ? OH addition to aromatic ring, abstraction of a H‐atom, and nucleophilic attack on the carbonyl group. The results showed that H‐atom abstraction pathways are the most favorable. The free energy change for H‐atom abstraction reaction ranges from ?37.8 to ?15.9 kcal/mol; for ? OH addition ranges from ?3.85 to ?1.23 kcal/mol; and for nucleophilic attack on the carbonyl group is 13.9 kcal/mol. The calculated rate constant between neutral ibuprofen and ? OH, 6.72 × 10⁹ M^?1s^?1, is consistent with the experimental value, 6.5 ± 0.2 × 10⁹ M^?1s^?1. Our results provide direct evidence for byproduct formation and identification on the molecular level. © 2013 Wiley Periodicals, Inc.     

Gas-phase acidity of D-glucose. A density functional theory study

The gas-phase acidity of D-glucopyranose was studied by means of B3LYP calculations combined with 6-31G(d,p) or 6-31+G(d,p) standard basis sets. For each anomer, deprotonation of the various primary and secondary hydroxyl groups was considered. As in solution, the anomeric hydroxyl is found to be the most acidic for both anomers, but only when the 6-31+G(d,p) basis set is used for geometry optimization. Deprotonation of the anomeric hydroxyl induces an important C(1)--O endocyclic bond elongation and subsequently promotes an energetically favored ring-opening process as attested by the very small calculated activation barriers. The results also suggest that interconversion between the various deprotonated alpha- and beta-anomers may easily occur under slightly energetic conditions. B3LYP/6-311+G(2df,2p) calculations led to the an absolute gas-phase acidity of deltaacidGo(298)(alpha-D-glucose) = 1398 kJ mol(-1). This estimate matches well the only experimental value available to date. Finally, this study again confirms that the use of diffuse functions on heavy atoms is necessary to describe anionic systems properly and to achieve good relative and absolute gas-phase acidities.     

Reactions of fullerene C60 with methyl methacrylate radicals: A density functional theory study

We have investigated the stepwise addition of four growing methyl methacrylate (MMA) radicals to C₆₀ fullerene, taking into account all possible types of the formed adducts. This reaction set is a reliable approximation for understanding the MMA polymerization process in the presence of C₆₀ fullerene. We have analyzed the structures of the fullerene-MMA adducts and energy parameters of their formation (heat effects and activation enthalpies). We found that up to three MMA growing radicals are favorably attached to C₆₀ as the fullerene-MMA trisadduct is a stable radical of the allyl type. It is inactive for further radical addition, and the elimination of the hydrogen atom from the growing MMA radical becomes preferable. The effects of steric factors and structures of the products of multiple growing MMA radical additions to C₆₀ on the radical polymerization of MMA in the presence of C₆₀ fullerene are considered.     

Modeling a halogen dance reaction mechanism: A density functional theory study

Since the discovery of the halogen dance (HD) reaction more than 60 years ago, numerous insights into the mechanism have been unveiled. To date however, the reaction has not been investigated from a theoretical perspective. Density functional theory (DFT) was used to model the potential energy surface linking the starting reagents to the lithiated products for each step in the mechanism using a thiophene substrate. It was found that the lithium‐halogen exchange mechanism is critical to understand the HD mechanism in detail and yielded the knowledge that S_N2 transition states (TS) are favored over the four‐center type for the lithium‐bromine exchange steps. The overall driving force for the HD is thermodynamics, while the kinetic factors tightly control the reaction path through temperature. The S_N2 lithium‐bromide TS are barrierless, except the second, which is the limiting step. Finally, the model for the HD is discovered to be a pseudo‐clock type, due to a highly favorable bromide catalysis step and the reformation of 2‐bromothiophene. © 2016 Wiley Periodicals, Inc.