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.     

Interactions between polymer brushes in solvents of variable quality: a density functional theory study

We present a density functional theory study of interactions between sterically stabilized colloidal particles in solvents of variable quality. Both flat and spherical polymer brushes are considered, as well as both monatomic and polymeric solvents. It is shown that the interaction between sterically stabilized particles can be tuned from repulsive to attractive by varying the solvent quality, the relative length of free and grafted chains, and by employing a mixed brush consisting of both well and poorly solvated chains.     

Interactions between colloidal particles in polymer solutions: A density functional theory study

We present a density functional theory study of colloidal interactions in a concentrated polymer solution. The colloids are modeled as hard spheres and polymers are modeled as freely jointed tangent hard sphere chains. Our theoretical results for the polymer-mediated mean force between two dilute colloids are compared with recent simulation data for this model. Theory is shown to be in good agreement with simulation. We compute the colloid-colloid potential of mean force and the second virial coefficient, and analyze the behavior of these quantities as a function of the polymer solution density, the polymer chain length, and the colloid/polymer bead size ratio.     

Modeling proton transfer in imidazole-like dimers: a density functional theory study

A detailed theoretical study of proton transfer reaction in protonated imidazole, 1,2,3-triazole, and tetrazole dimers, the basic components of polymeric membrane used in proton exchange membranes fuel cells, has been carried out. In particular, several approaches based on density functional theory have been considered and their results compared with those provided by post-HF methods. From a computational point of view, these molecules appear to be a very challenging playground also for robust and recent functionals. Indeed none of the considered approaches provide results in close agreement with the reference post-HF data and a combined BMK//B3LYP model seems the only approach able to reproduce both the energetic and the structural features. From a chemical point of view, two new mechanisms of proton transfer in tetrazole dimers have been investigated and found to be more favorable than that previously hypothesized in literature. At the same time, the theoretical results show a direct connection between the obtained proton transfer barrier and the charge localized on the transferred hydrogen.     

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.     

Surface forces in polymer fluids: a comparison between simulations and density functional theory

A polymer density functional theory is evaluated in terms of its ability to predict interactions between large surfaces in a polymer fluid. Comparisons are made with results from simulations in an expanded isotension ensemble. The variation of the net surface-surface interaction with adsorption strength is examined. Cases where the monomers interact via a pure hard sphere potential are investigated, but we have also studied the effect of attractions between the monomers. In all cases, we obtain an almost quantitative agreement between the simulated results and the predictions from the polymer density functional theory.     

Interactions between colloidal particles in amphiphilic mixtures: a density functional theory study

We present a density functional theory study of interactions between spherical colloidal particles in amphiphile solutions. Theory is found to be in good agreement with previously published molecular dynamics simulations. It is used to analyze the effect of the amphiphile solution bulk density, the chain length, and the solvent mole fraction on the potential of mean force between the particles. The general features of the potential of mean force are rationalized in terms of formation of layers and bilayers of amphiphilic molecules in the intercolloidal gap. Theory yields the same general trends as observed in simulations and in experiments. In particular, the computed mean force changes its character from repulsive to attractive and back to repulsive as the solvent mole fraction is gradually increased.     

Density functional theory study of the interaction between formamide and uracil

The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6‐31G to 6‐311++G(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven‐membered rings; the others are eight‐membered rings. The eight‐membered ring is preferred over the seven‐membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

肾上腺素与胞嘧啶相互作用的密度泛函理论研究

采用密度泛函理论（DFT）B3LYP方法和6-311＋G（d,p）基组对肾上腺素-胞嘧啶复合物进行结构优化和频率计算,得到15种稳定的复合物.研究发现,所有的复合物进行基组重叠误差（BSSE）校正后的相互作用能为-11.43^-48.96kJ/mol,符合氢键能量范围,相互作用能主要由氢键所贡献.结构和振动频率分析显示,氢键的形成使相应O（N）—H键的键长变长,对称伸缩振动频率减小,说明复合物中形成的氢键都是正常的红移型氢键.应用自然键轨道（NBO）理论和分子中的原子（AIM）理论对15种复合物的氢键性质和特征进行分析,发现氢键对于复合物的稳定性起着重要作用,当复合物形成2个或更多的氢键时,氢键的数目、类型及强度共同决定着复合物的稳定性,复合物基本符合三氢键〉二氢键〉单氢键的稳定顺序,三氢键复合物4是最稳定的,复合物3存在单氢键O—H…O,比部分二氢键复合物要稳定.     

儿茶素-胞嘧啶分子间相互作用的密度泛函研究

采用密度泛函理论的B3LYP方法,在6-31+G*基组水平上研究了儿茶素-胞嘧啶分子间相互作用机制,得到稳定的儿茶素-胞嘧啶复合物11个.计算结果表明氢键对于复合物的稳定性起着重要的作用,并且当复合物形成2个或更多的氢键时,氢键的类型及强度共同决定着复合物的稳定性.我们还应用了分子中的原子(AIM)理论和自然键轨道(NBO)理论对这11种复合物中氢键的性质和特征进行了分析.通过研究发现,所有的氢键复合物进行基组重叠误差(BSSE)校正后的相互作用能为-17.35～-43.27kJ/mol,相互作用能主要由氢键所贡献.振动分析显示,氢键的形成使相对应键的对称伸缩振动频率减小,说明这些复合物中形成的氢键都是正常的红移型氢键,与实验结果相一致.     

Hydrogen-bonding interaction of urea with DNA bases: A density functional theory study

This work deals with the interaction between urea and DNA bases (adenine, thymine, guanine, and cytosine). The optimized geometries, binding energies, and harmonic vibrational frequencies are calculated using the DFT/B3LYP functional combined with the 6–31+G(d,p) basis set. Their interactions are studied aiming to understand more about the nature of the intercalation binding forces between urea and DNA. Fourteen stable complexes are found on the potential energy surface. The structures are cyclic; they are stabilized by NH...O/N and CH...O interactions. The binding energies range from −19.9 kJ·mol⁻¹ to −74.0 kJ·mol⁻¹. The obtained formation energies indicate that Urea:G and Urea:C are more favorable than Urea:T and Urea:A. In addition, the Atoms in Molecules theory is performed to study the hydrogen bonds in the complexes.     

Adsorbate-substrate interaction between chlorodifluoromethane and titanium dioxide: Infrared spectroscopy and density functional theory studies

Infrared spectra of chlorodifluoromethane (CHClF₂) adsorbed on titanium dioxide (TiO₂) at room temperature have been investigated for the first time. From the comparison between the adsorption characteristics and the gas-phase spectra it can be deduced that the molecule interacts with the surface Lewis acid site (Ti⁴⁺) mainly through the Cl atom even if also the adsorption with one F atom is also observed. Moreover, the spectra show the presence of H-bonds between the CH group and the surface Lewis basic site (OH⁻ or O²⁻). In order to obtain more information on the molecule orientation and the variation of the structural parameters, a DFT-B3LYP study has been carried out considering the anatase (1 0 1) surface and evaluating the adsorption energetics in terms of interaction, distortion and binding energies. The obtained geometries confirm that both the acid-base interactions through Cl or F atoms are possible and suggest the formation of one H-bond between the CH group of the molecule and the Lewis basic site of the surface. The calculated vibrational frequencies of the adsorbed molecule have been found to be in reasonable agreement with the experimental data.     

Configuration interaction based on constrained density functional theory: a multireference method

Existing density functional theory (DFT) methods are typically very effective in capturing dynamic correlation, but run into difficulty treating near-degenerate systems where static correlation becomes important. In this work, we propose a configuration interaction (CI) method that allows one to use a multireference approach to treat static correlation but incorporates DFT's efficacy for the dynamic part as well. The new technique uses localized charge or spin states built by a constrained DFT approach to construct an active space in which the effective Hamiltonian matrix is built. These local configurations have significantly less static correlation compared to their delocalized counterparts and possess an essentially constant amount of self-interaction error. Thus their energies can be reliably calculated by DFT with existing functionals. Using a small number of local configurations as different references in the active space, a simple CI step is then able to recover the static correlation missing from the localized states. Practical issues of choosing configurations and adjusting constraint values are discussed, employing as examples the ground state dissociation curves of H(2) (+), H(2), and LiF. Excellent results are obtained for these curves at all interatomic distances, which is a strong indication that this method can be used to accurately describe bond breaking and forming processes.     

Modeling the action of an antitumor drug: a density functional theory study of the mechanism of tirapazamine

Density functional theory methods are employed to investigate experimentally proposed mechanisms by which the antitumor drug tirapazamine may react with a DNA sugar-C(1)' radical to give the sugar derivative deoxyribonolactone, with concomitant DNA strand breakage. For the previously proposed minor pathway, ionization of the sugar-C(1)' radical by tirapazamine, the calculated ionization energy, and the electron affinity of the models of the sugar-C(1)' radical of DNA and tirapazamine suggest that tirapazamine must be protonated to be able to oxidize the sugar-C(1)' radical. The preferred mechanism for reaction of tirapazamine with a sugar-C(1)' radical, in agreement with experimental observations, is found to proceed by direct attack of an N-oxide oxygen of tirapazamine at the sugar-C(1)' position, followed by homolytic cleavage of the N-O bond of the drug moiety. Possible alternative mechanisms are also investigated.     

Raman scattering in crystalline oligothiophenes: a comparison between density functional theory and bond polarizability model

Raman intensity of intramolecular and lattice modes of crystalline alpha-bithiophene (alpha-2T) are investigated within density functional theory using a nonlinear response formalism. First, comparison between the calculated Raman spectrum and the experimental data allows the assignment of the main Raman lines over the whole frequency range. Then, a bond polarizability (BP) model, limited to first neighbors, is built. We show that, although the BP model cannot reproduce the changes of dielectric susceptibility under individual atomic displacements, it is accurate enough to reproduce the profile of the unpolarized nonresonant Raman spectrum of alpha-2T powder. Finally, the BP model, fitted on our first-principles results on alpha-2T, is applied with success to the alpha-quaterthiophene polymorph phases and alpha-sexithiophene, demonstrating on practical examples that first-principles and BP approaches are powerful complementary tools to calculate the nonresonant Raman spectrum of alpha-2T and make reasonable predictions on larger oligothiophenes.     

Regioselectivity for condensation reactions of quinonoid models of tryptophan tryptophylquinone: a density functional theory study

The model compounds of tryptophan tryptophylquinone (TTQ), o-benzoquinone (OBQ), 3-methyl-6,7-dihydro-1H-6,7-indoledione (MIQ), and 3-methyl-4-(3-methyl-1H-2-indolyl)-6,7-dihydro-1H-6,7-indoledione (IIQ), all of which are characteristic of o-quinone groups, have been studied with density functional theory. The dihedral angle of the two indole rings (chi) of IIQ is calculated to be 49.6 degrees for the global minimum. Another local minimum, 0.74 kcal/mol higher in energy, with a chi value of 123.5 degrees is also fully optimized. The transition state connecting the two minima, with a chi value of 97.9 degrees, has been located and the rotation barrier is 1.71 kcal/mol. A scan of the potential energy surface along this dihedral angle showed that the difference of the total energy was within 1.0 kcal/mol at a range of the dihedral angle from 30 degrees to 75 degrees. Hence, IIQ is flexible for the rotation of inter-indole rings. The origin of regioselectivity for the condensation reactions of the models MIQ and IIQ with NH(3) has been elucidated. It is shown that the energy difference between the two different types of carbinolamine intermediates (Delta E) and their corresponding transition structures (Delta E(++)) should be responsible for the regioselectivity. To assess the effect of the fused ring on regioselectivity of the condensation reaction, a series of models were designed. A good linear correlation has been found between the energy difference of the two different carbinolamine intermediates (Delta E) and that of the corresponding transition states (Delta E(++)), suggesting that the factors that stabilize the carbinolamine intermediate also favor the stability of the corresponding transition structure. The pair, 6-amino-6-hydroxy-8-methyl-6H-quinolin-5-one and 5-amino-5-hydroxy-8-methyl-5H-quinolin-6-one (7/8), deviates from the correlation and represents some anomalous behavior, which may be due to their structural particularity. It also has been shown that the tricyclic models, which consist of OBQ and two fused heterocyclic rings, represent more regioselectivity in contrast to the bicyclic systems. Moreover, the fused electron-donating pyrrole and the fused electron-withdrawing pyridine or pyrimidine show a somewhat synergistic effect on each other via the medial OBQ molecule. The barrier of the condensation reaction for pyrrolo[2,3-f]quinoline-4,5-dione is calculated to be ca. 22 kcal/mol. This is lower than that for MIQ (ca. 33 kcal/mol) and IIQ (ca. 32 kcal/mol) by as much as 10.0 kcal/mol, explaining reasonably the larger catalytic effect of pyrroloquinolinequinone (PQQ) relative to TTQ.     

Substituent effects on benzdiyne: a density functional theory study

Density functional theory (DFT) studies were performed to investigate the effect of substituents on the properties of benzdiyne derivatives. Twelve substituted benzdiynes-C(6)X(2), where X = F, Cl, Br, Me, CF(3), CN, OH, NO(2), NH(2), OMe, NMe(2), and Ph-were considered along with the unsubstituted 1,4-benzdiyne. The structures, vibrational frequencies, and IR intensities of these benzdiynes were studied with a popular three-parameter hybrid density functional (B3LYP) combined with the split-valence 6-31G(d) basis set and Dunning's correlation-consistent polarized triple-zeta (cc-pVTZ) basis set. The relative stabilities of the substituted benzdiynes were studied with the help of reaction energies of isodesmic reactions, which showed that the electron-withdrawing groups destabilized the benzdiynes more than they did the corresponding benzenes, whereas the electron-donating groups stabilized the benzdiynes more than they did their benzene counterparts. Correlation analyses revealed that field/inductive effects played a more important role than did resonance effects. The changes in atomic charges and spin populations due to the substituents were also studied. The asymmetric nu(Ctbd1;C) stretching modes obtained were close to the 1500-cm(-)(1) mark. Reinvestigation of the experimental results supported these results; a weak IR band at 1486 cm(-)(1) was assigned to this asymmetric stretching mode in C(6)(CF(3))(2) F. Some other benzdiynes also had large IR intensity values for their asymmetric nu(Ctbd1;C) vibrational modes due to the coupling with other vibrational modes. Heats of formation for the substituted benzdiynes were obtained from the reaction energies calculated at the B3LYP/cc-pVTZ level of theory.     

Mechanisms of difluoroethylene ozonolysis: a density functional theory study

We present a density functional theory (DFT) study on the mechanisms of gas-phase ozonolysis of three isomers of difluoroethylene, namely, cis-1,2-difluoroethylene, trans-1,2-difluoroethylene, and 1,1-difluoroethylene. MPW1K/cc-pVDZ and BHandHLYP/cc-pVDZ methods are employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points were further refined at the QCISD(T)/cc-pVDZ and QCISD(T)/6-31+G(df,p) levels of theory with zero-point energy (ZPE) corrections. The ozone-cis-1,2-difluoroethylene reaction is predicted to be slower than the ozone-trans-1,2-difluoroethylene reaction. The enhanced reactivity of trans-1,2-difluoroethylene relative to the cis isomer is similar to the reactions of ozone with cis- and trans-dichloroethylene. The ozone-1,1-difluoroethylene reaction is predicted to be slower than the ozone-trans-1,2-difluoroethylene reaction. These results are in agreement with experimental studies. The calculated mechanisms indicate that in ozone-difluoroethylene reactions the yields of OH might be trivial, which is different from the reactions of ozone with unsaturated hydrocarbons.     

Density functional theory study on the interaction between metalloporphyrins and NH3

The binding behaviors of eight bivalent metalloporphyrins (MPs) (M?Zn, Mg, Cu, Mn, Fe, Co, Ni, and Cd) with NH₃ were investigated by density functional theory. For both MPs and corresponding complexes MPs‐NH₃, good linear correlations are found between the partial charge on metal M and that on atom N (nitrogen of porphyrin) as well as the M? N bond length. Natural population and frontier orbital analysis demonstrate that charge transfer in CoP‐NH₃ is much easier and greater. As a consequence of the charge transfer and the hybridization of molecular energy levels, striking disparities of electronic properties of MPs‐NH₃ are observed. Particularly, a modest linear relationship is obtained between the magnitude of charge transfer and the binding energy. The much greater Fukui functions of CoP, together with its larger binding strength, suggest that CoP is more favorable to the interaction with NH₃, which might be a promising sensing material to response NH₃. © 2013 Wiley Periodicals, Inc.     

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution.