Oligo(vinylidene fluoride) Langmuir-Blodgett films studied by spectroscopic ellipsometry and the density functional theory

Thin films of amphiphilic vinylidene fluoride oligomers prepared by Langmuir-Blodgett deposition on silicone substrates were investigated by comparing experimental and theoretical mid-infrared (IR) spectra. The experimental spectra were obtained using infrared spectroscopic ellipsometry. Theoretical spectra were calculated using density functional theory. Excellent correspondence of major IR bands in both data sets shows that the molecular backbone is oriented with the long axis normal to the substrate plane. This is in contrast to poly(vinylidene fluoride) LB films, in which the polymer chains are parallel to the substrate.     

Location of Mg cations in mordenite zeolite studied by IR spectroscopy and density functional theory simulations with a CO adsorption probe

The location of Mg cations in the channel of mordenite zeolite was studied using a combination of DFT simulations and IR spectroscopy of adsorbed CO. The calculated adsorption energies and frequencies of CO on Mg cations are in good agreement with the results from the IR spectra of adsorbed CO. It is found that the Mg cations can occupy the sites A, C, D and E in mordenite and the distribution of the Mg cations in these sites follows the priority order, site C > site A > site D and site E.     

Water cluster anions studied by the long-range corrected density functional theory

Long-range corrected density functional theory (LC-DFT) is applied to a series of small water cluster anions(n= 2-6) to compute their vertical detachment energies (VDEs). The LC scheme is shown to eliminate an unphysical overestimation of the electron-water attraction in the hybrid functional by properly accounting for the long-range exchange repulsions. It is shown that a correct correlation energy behavior for a rapidly varying density is also important for describing a spatially extent, excess electron. The one-parameter progressive (OP) correlation functional, which satisfies this condition, leads to a remarkable improvement in the calculated VDE over the conventional one. The LC-BOP method produces highly accurate VDEs with a mean absolute deviation of 13.8 meV from the reference CCSD(T) results, reducing the error of B3LYP by more than 15 times. LC-BOP is found to be more accurate than MP2 which yields an excess electron underbound by 43.6 meV. The effect of basis sets on the calculated VDE is also examined. The aug-cc-pVDZ basis set with an extra diffuse function is found to be more accurate and reliable than the extended Pople-type basis sets used in the previous works. The extrapolation of the calculated VDE of different electron binding motifs is compared with the VDEs of experimentally observed three isomers (Verlet, J. R. R.; Bragg,A. E.; Kammrath, A.; Cheshnovsky, O.; Neumark, D. M. Science 2005, 307, 93).     

Multicoefficient density functional theory (MC-DFT)

We have systematically tested the performance of several pure and hybrid versions of density functional methods on different types of molecular energies by combining energies calculated using more than one basis sets. Most hybrid functionals show important performance improvement as compared to methods using only a single basis set. The results suggest that, in many cases, scaling the basis set corrections is also important for density functional theory calculation. The best method, the B1B95 functional using the cc-pVDZ/cc-pVTZ/aug-cc-pVDZ basis set combination, achieves an average accuracy of 1.76 kcal/mol on a database of 109 atomization energies, 38 hydrogen-transfer barrier heights, 38 non-hydrogen-transfer barrier heights, 13 ionization potentials, and 13 electron affinities.     

Photophysical properties of natural light-harvesting complexes studied by subsystem density functional theory

In this study, we investigate the excited states and absorption spectra of a natural light-harvesting system by means of subsystem density functional theory. In systems of this type, both specific interactions of the pigments with surrounding protein side chains as well as excitation energy transfer (EET) couplings resulting from the aggregation behavior of the chromophores modify the photophysical properties of the individual pigment molecules. It is shown that the recently proposed approximate scheme (J. Chem. Phys. 2007, 126, 134116) for coupled excitations within a subsystem approach to time-dependent DFT is capable of describing both effects in a consistent manner, and is efficient enough to study even the large assemblies of chromophores occurring in the light-harvesting complex 2 (LH2) of the purple bacterium Rhodopseudomonas acidophila. A way to extract phenomenological coupling constants as used in model calculations on EET rates is outlined. The resulting EET coupling constants and spectral properties are in reasonable agreement with the available reference data. Possible problems related to the effective exchange-correlation kernel are discussed.     

Dinuclear Zn(II) complex catalyzed phosphodiester cleavage proceeds via a concerted mechanism: a density functional theory study

Density functional theory (DFT) calculations were used to study the mechanism for the cleavage reaction of the RNA analogue HpPNP (HpPNP = 2-hydroxypropyl-4-nitrophenyl phosphate) catalyzed by the dinuclear Zn(II) complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (Zn(2)(L(2)O)). We present a binding mode in which each terminal phosphoryl oxygen atom binds to one zinc center, respectively, and the nucleophilic 2-hydroxypropyl group coordinates to one of the zinc ions, while the hydroxide from deprotonation of a water molecule coordinates to the other zinc ion. Our calculations found a concerted mechanism for the HpPNP cleavage with a 16.5 kcal/mol reaction barrier. An alternative proposed stepwise mechanism through a pentavalent oxyphosphorane dianion reaction intermediate for the HpPNP cleavage was found to be less feasible with a significantly higher energy barrier. In this stepwise mechanism, the deprotonation of the nucleophilic 2-hydroxypropyl group is accompanied with nucleophilic attack in the rate-determining step. Calculations of the nucleophile (18)O kinetic isotope effect (KIE) and leaving (18)O KIE for the concerted mechanism are in reasonably good agreement with the experimental values. Our results indicate a specific-base catalysis mechanism takes place in which the deprotonation of the nucleophilic 2-hydroxypropyl group occurs in a pre-equilibrium step followed by a nucleophilic attack on the phosphorus center. Detailed comparison of the geometric and electronic structure for the HpPNP cleavage reaction mechanisms in the presence/absence of catalyst revealed that the catalyst significantly altered the determining-step transition state to become far more associative or tight, that is, bond formation to the nucleophile was remarkably more advanced than leaving group bond fission in the catalyzed mechanism. Our results are consistent with and provide a reliable interpretation for the experimental observations that suggest the reaction occurs by a concerted mechanism (see Humphry, T.; Iyer, S.; Iranzo, O.; Morrow, J. R.; Richard, J. P.; Paneth, P.; Hengge, A. C. J. Am. Chem. Soc. 2008, 130, 17858-17866) and has a specific-base catalysis character (see Yang, M.-Y.; Iranzo, O.; Richard, J. P.; Morrow, J. R. J. Am. Chem. Soc. 2005, 127, 1064-1065).     

Molecular electronegativity in density functional theory(VIII)

Based on the density functional theory and the atom-bond electronegativity equalization model (ABEEM), a method is proposed to construct the softness matrix and to obtain the electron population normal modes (PNMs) for a closed system. Using this method the information about the bond charge polarization in a molecule can be obtained easily. The test calculation shows that the PNM obtained by this method includes all the modes about the bond charge polarization explicitly. And the bond charge polarization mode characterized by the biggest eigenvalue, which is the softest one of all modes related with chemical bonds, can describe the charge polarization process in a molecule as exquisitely as the correspondingab initio method.     

Molecular electronegativity in density functional theory (VI)

Based on the density functional theory and partitioning the molecular electron density ρ (r) into atomic electronic densities and bond electronic densities, the expressions of the total molecular energy and the “effective electronegativity” of an atom or a bond in a molecule are obtained. The atom-bond electronegativity equalization model is then proposed for the direct calculation of the total molecular energy and the charge distribution of large molecules. Practical calculations show that the atom-bond electronegativity equalization model can reproduce the correspondingab initio values of the total molecular energies and charge distributions for a series of large molecules with a very satisfactory accuracy.     

Solvation and crystal effects in bilirubin studied by NMR spectroscopy and density functional theory

The open-chain tetrapyrrole compound bilirubin was investigated in chloroform and dimethyl sulfoxide solutions by liquid-state NMR and as solid by (1)H, (13)C, and (15)N magic-angle spinning (MAS) solid-state NMR spectroscopy. Density functional theory (DFT) calculations were performed to interpret the data, using the B3LYP exchange-correlation functional to optimize geometries and to compute NMR chemical shieldings by the gauge-including atomic orbital method. The dependence of geometries and chemical shieldings on the size of the basis sets was investigated for the reference molecules tetramethylsilane, NH(3), and H(2)O, and for bilirubin as a monomer and in clusters consisting of up to six molecules. In order to assess the intrinsic errors of the B3LYP approximation in calculating NMR shieldings, complete basis set estimates were obtained for the nuclear shielding values of the reference molecules. The experimental liquid-state NMR data of bilirubin are well reproduced by a monomeric bilirubin molecule using the 6-311+G(2d,p) basis set for geometry optimization and for calculating chemical shieldings. To simulate the bilirubin crystal, a hexameric model was required. It was constructed from geometry-optimized monomers using information from the X-ray structure of bilirubin to fix the monomeric entities in space and refined by partial optimization. Combining experimental (1)H-(13)C and (1)H-(15)N NMR correlation spectroscopy and density functional theory, almost complete sets of (1)H, (13)C, and (15)N chemical shift assignments were obtained for both liquid and solid states. It is shown that monomeric bilirubin in chloroform solution is formed by 3-vinyl anti conformers, while bilirubin crystals are formed by 3-vinyl syn conformers. This conformational change leads to characteristic differences between the liquid- and solid-state NMR resonances.     

Interfacial colloidal sedimentation equilibrium. II. Closure-based density functional theory

In Part I [R. E. Beckham and M. A. Bevan, J. Chem. Phys. 127, 164708 (2007)], results were presented for the sedimentation equilibrium of concentrated colloidal dispersions using confocal scanning laser microscopy experiments, Monte Carlo (MC) simulations, and a local density approximation perturbation theory. In this paper, we extended the modeling effort on those systems to include nonlocal density functional theory (DFT), which is capable of predicting the microstructure of the sediment at length scales comparable to the colloidal particle dimension. Specifically, we use a closure-based DFT formulation to predict interfacial colloidal sedimentation equilibrium density profiles. The colloid-colloid and colloid-surface interactions were modeled with DLVO screened electrostatic potentials using parameters taken directly from the experimental work. The DFT profiles were compared to the experimental and MC results from Part I. Good agreement was found for relatively dilute interfacial colloidal fluids, but agreement was less satisfactory as interfacial layering became more pronounced for conditions approaching the onset of interfacial crystallization. We also applied DFT in an inverse sense using the measured colloid density profile to extract the underlying colloid-surface potential; this can be thought of as a microscopic analog to the well-known procedure of using the macroscopic (coarse-grained) density profile to extract the osmotic equation of state. For the dilute interfacial fluid, the inverse DFT calculations reproduced the true colloid-surface potential to within 0.5kT at all elevations.     

Excited state property of hardly photodissociable heme-CO adduct studied by time-dependent density functional theory

While most of CO-bound hemes are easily photodissociated with a quantum yield of nearly unity, we occasionally encounter a CO-heme which appears hardly photodissociable under the ordinary measurement conditions of resonance Raman spectra using CW laser excitation and a spinning cell. This study aims to understand such hemes theoretically, that is, the excited-state properties of the five-coordinate heme-CO adduct (5cH) as well as the 6c heme-CO adduct (6cH) with a weak axial ligand. Using a hybrid density functional theory, we scrutinized the properties of the ground and excited spin states of the computational models of a 5cH and a water-ligated 6cH (6cH-H(2)O) and compared these properties with those of a photodissociable imidazole-ligated 6cH (6cH-Im). Jahn-Teller softening for the Fe-C-O bending potential in the a(1)-e excited state was suggested. The excited-state properties of 6cH-Im and 5cH were further studied with time-dependent DFT theory. The reaction products of 6cH-Im and 5cH were assumed to be quintet and triplet states, respectively. According to the time-dependent DFT calculations, the Q excited state of 6cH-Im, which is initially a pure pi-pi state, crosses the Fe-CO dissociative state (2A') without large elongation of the Fe-CO bond. In contrast, the Q state of the 5cH does not cross the Fe-CO dissociative state but results in the formation of the excited spin state with a bent Fe-C-O. Consequently, photoisomerization from linear to bent Fe-C-O in the 5cH is a likely mechanism for apparent nonphotodissociation.     

烷基吡啶及氯化铝正负离子结构的密度泛函研究

采用量子化学密度泛函方法对N-烷基吡啶阳离子和阴离子AlCl4-,Al2Cl7-和Al3Cl10-进行了全优化计算,得到了阴阳离子的几何构型和净电荷分布.计算发现,吡啶环上的电子数符合4n 2规则,具有芳香性.吡啶阳离子的LUMO轨道主要由环上原子的2pz所贡献,是反键π分子轨道.AlCl4-,Al2Cl7-和Al3Cl10-的HOMO轨道主要由Cl原子的2px所贡献.推测吡啶阳离子的LUMO与阴离子的HOMO相互作用形成离子液体分子.     

Molecular structure and spectroscopic studies on novel complexes of coumarin-3-carboxylic acid with Ni(II), Co(II), Zn(II) and Mn(II) ions based on density functional theory

Novel Ni(II), Co(II), Zn(II) and Mn(II) complexes of coumarin-3-carboxylic acid (HCCA) were studied at experimental and theoretical levels. The complexes were characterised by elemental analyses, FT-IR, (1)H NMR, (13)C NMR and UV-Vis spectroscopy and by magnetic susceptibility measurements. The binding modes of the ligand and the spin states of the metal complexes were established by means of molecular modelling of the complexes studied and calculation of their IR, NMR and absorption spectra at DFT(TDDFT)/B3LYP level. The experimental and calculated data verified high spin Ni(II), Co(II) and Mn(II) complexes and a bidentate binding through the carboxylic oxygen atoms (CCA2). The model calculations predicted pseudo octahedral trans-[M(CCA2)(2)(H(2)O)(2)] structures for the Zn(II), Ni(II) and Co(II) complexes and a binuclear [Mn(2)(CCA2)(4)(H(2)O)(2)] structure. Experimental and calculated (1)H, (13)C NMR, IR and UV-Vis data were used to distinguish the two possible bidentate binding modes (CCA1 and CCA2) as well as mononuclear and binuclear structures of the metal complexes.     

Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1) H and (13) C?NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13) C and (1) H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.     

Effect of halides and alkali cations on the Zn(Hg)/Zn(II) electrode reactions

The title subject has been studied by galvanostatic single-pulse, chronopotentiometric and equilibrium measurements on the Zn(Hg)/Zn(II) electrode in x M KI+(1?x) M KCl (x from 0 to 1), 1 M KBr and 1 M MeCl (Me=Li, Na, K and Cs) solutions of pH 3 at 25°C. Quantitative information about the effect of specifically adsorbed halides on the rates of the Zn(II)/Zn(I) and the Zn(I)/Zn(Hg) steps is obtained separately (for the latter step mainly at potentials near ?1.0 V(SCE)), and the latter step seems to be more influenced than the former by the adsorption. An attempt is made to correlate the adsorption effect on the rate of the Zn(II)/Zn(I) step to double-layer parameters according to recent models for such effects. The extra current observed at potentials where the halides are adsorbed, seems to vary with the surface activity of the specifically adsorbed ion. The lack of any observed kinetic effect of Cs⁺, which is specifically adsorbed at these potentials, is possibly due to the Cs⁺ specific adsorption enhancing the Cl^? specific adsorption and vice versa, so that the decelerating and accelerating effects by these ions may cancel each other.     

Conduction of Li+ cations in ethylene carbonate (EC) and propylene carbonate (PC): comparative studies using density functional theory

Density functional theory is used to study the interaction of Li⁺ cation with ethylene carbonate (EC) and propylene carbonate (PC) comparatively, which are the most popular solvents used in lithium-ion battery composite. In our theoretical calculations, we use DFT hybrid parameter B3LYP5 with a basis set 6–31G** by means of PCGAMESS/Firefly software package. We analyze the optimized structures of EC, PC, and their clusters including lithium-ion. We then calculate solvation energy, desolvation energy, electron affinity, Gibbs free energy, heats of formation of Li⁺ solvated by EC and PC, and the charge on Li⁺. From the above analysis, we observe EC as a better solvent than PC in applications of lithium-ion batteries.     

Valence electronic structure of benzo-2,1,3-chalcogenadiazoles studied by photoelectron spectroscopy and density functional theory

The He I photoelectron spectra of benzo-2,1,3-thia-, selena-, and telluradiazole were measured, and the observed ionization bands were assigned by comparison with the results of DFT calculations. Whereas the B3LYP exchange-correlation functional provided orbital energies that permitted a preliminary assignment by application of Koopman's theorem, a more-accurate interpretation was established by calculation of the vertical ionization energies with the PW91 functional and analysis of the correlation of energy levels along the homologous series. This strategy clarified earlier disagreements in the assignment of the spectrum of benzo-2,1,3-thiadiazole.     

Geometry, reduction potential, and reorganization energy of the binuclear Cu(A) site, studied by density functional theory

The dimeric Cu(A) site found in cytochrome c oxidase and nitrous oxide reductase has been studied with the density functional B3LYP method. We have optimized the structure of the realistic (Im)(S(CH(3))(2))Cu(SCH(3))(2)Cu(Im)(CH(3)CONHCH(3)) model in the fully reduced, mixed-valence, and fully oxidized states. The optimized structures are very similar to crystal structures of the protein, which shows that the protein does not strain the site significantly. Instead, inorganic model complexes of the protein site are strained by the macrocyclic connections between the ligand models. For the mixed-valence (Cu(I)+Cu(II)) state, two distinct equilibrium structures were found, one with a short Cu-Cu distance, 248 pm, similar to the protein structure, and one with a longer distance, 310 pm, similar to what is found in inorganic models. In the first state, the unpaired electron is delocalized over both copper ions, whereas in the latter, it is more localized to one of the ions. The two states are nearly degenerate. The potential energy surfaces for the Cu-Cu, Cu-S(Met), and Cu-O interactions are extremely flat. In fact, all three distances can be varied between 230 and 310 pm at an expense in energy of less than 8 kJ/mol, which explains the large variation observed in crystal structures for these interactions. Inclusion of solvation effects does not change this significantly. Therefore, we can conclude that a variation in these distances can change the reduction potential of the Cu(A) site by at most 100 mV. The model complex has a reorganization energy of 43 kJ/mol, 20 kJ/mol lower than for a monomeric blue-copper site. This lowering is caused by the delocalization of the unpaired electron in the mixed-valence state.