A new all-round density functional based on spin states and SN2 barriers

We report here a new empirical density functional that is constructed based on the performance of OPBE and PBE for spin states and SN 2 reaction barriers and how these are affected by different regions of the reduced gradient expansion. In a previous study [Swart, Sol̀, and Bickelhaupt, J. Comput. Methods Sci. Eng. 9, 69 (2009)] we already reported how, by switching between OPBE and PBE, one could obtain both the good performance of OPBE for spin states and reaction barriers and that of PBE for weak interactions within one and the same (SSB-sw) functional. Here we fine tuned this functional and include a portion of the KT functional and Grimme's dispersion correction to account for π- π stacking. Our new SSB-D functional is found to be a clear improvement and functions very well for biological applications (hydrogen bonding, π -π stacking, spin-state splittings, accuracy of geometries, reaction barriers)

Ab initio benchmark study for the oxidative addition of CH4 to Pd: importance of basis-set flexibility and polarization

To obtain a state-of-the-art benchmark potential energy surface (PES) for the archetypal oxidative addition of the methane C-H bond to the palladium atom, we have explored this PES using a hierarchical series of ab initio methods (Hartree-Fock, second-order Møller-Plesset perturbation theory, fourth-order Møller-Plesset perturbation theory with single, double and quadruple excitations, coupled cluster theory with single and double excitations (CCSD), and with triple excitations treated perturbatively [CCSD(T)]) and hybrid density functional theory using the B3LYP functional, in combination with a hierarchical series of ten Gaussian-type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four-component all-electron approach. Counterpoise corrected relative energies of stationary points are converged to within 0.1-0.2 kcal/mol as a function of the basis-set size. Our best estimate of kinetic and thermodynamic parameters is -8.1 (-8.3) kcal/mol for the formation of the reactant complex, 5.8 (3.1) kcal/mol for the activation energy relative to the separate reactants, and 0.8 (-1.2) kcal/mol for the reaction energy (zero-point vibrational energy-corrected values in parentheses). This agrees well with available experimental data. Our work highlights the importance of sufficient higher angular momentum polarization functions, f and g, for correctly describing metal-d-electron correlation and, thus, for obtaining reliable relative energies. We show that standard basis sets, such as LANL2DZ+ 1f for palladium, are not sufficiently polarized for this purpose and lead to erroneous CCSD(T) results. B3LYP is associated with smaller basis set superposition errors and shows faster convergence with basis-set size but yields relative energies (in particular, a reaction barrier) that are ca. 3.5 kcal/mol higher than the corresponding CCSD(T) values

Exploring chromium (VI) dioxodihalides chemistry: is density functional theory the most suitable tool?

A comparative systematic study of the CrO2F2 compound has been performed using different conventional ab initio methodologies and density functional procedures. Two points have been analyzed: first, the accuracy of results yielded by each method under study, and second, the computational cost required to reach such results. Weighing up both aspects, density functional theory has been found to be more appropriate than the Hartree-Fock (HF) and the analyzed post-HF methods. Hence, the structural characterization and spectroscopic elucidation of the full CrO2X2 series (X=F,Cl,Br,I) has been done at this level of theory. Emphasis has been given to the unknown CrO2I2 species, and specially to the UV/visible spectra of all four compounds. Furthermore, a topological analysis in terms of charge density distributions has revealed why the valence shell electron pair repulsion model fails in predicting the molecular shape of such CrO2X2 complexes

Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31 G* and extended 6-31++ G* basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack

Density functional energy decomposition into one- and two-atom contributions

The present work provides a generalization of Mayer's energy decomposition for the density-functional theory (DFT) case. It is shown that one- and two-atom Hartree-Fock energy components in Mayer's approach can be represented as an action of a one-atom potential VA on a one-atom density ρ A or ρ B. To treat the exchange-correlation term in the DFT energy expression in a similar way, the exchange-correlation energy density per electron is expanded into a linear combination of basis functions. Calculations carried out for a number of density functionals demonstrate that the DFT and Hartree-Fock two-atom energies agree to a reasonable extent with each other. The two-atom energies for strong covalent bonds are within the range of typical bond dissociation energies and are therefore a convenient computational tool for assessment of individual bond strength in polyatomic molecules. For nonspecific nonbonding interactions, the two-atom energies are low. They can be either repulsive or slightly attractive, but the DFT results more frequently yield small attractive values compared to the Hartree-Fock case. The hydrogen bond in the water dimer is calculated to be between the strong covalent and nonbonding interactions on the energy scale

Desenvolupament computacional de la semblança molecular quàntica

La present Tesi Doctoral, titulada desenvolupament computacional de la semblança molecular quàntica, tracta, fonamentalment, els aspectes de càlcul de mesures de semblança basades en la comparació de funcions de densitat electrònica.El primer capítol, Semblança quàntica, és introductori. S'hi descriuen les funcions de densitat de probabilitat electrònica i llur significança en el marc de la mecànica quàntica. Se n'expliciten els aspectes essencials i les condicions matemàtiques a satisfer, cara a una millor comprensió dels models de densitat electrònica que es proposen. Hom presenta les densitats electròniques, mencionant els teoremes de Hohenberg i Kohn i esquematitzant la teoria de Bader, com magnituds fonamentals en la descripció de les molècules i en la comprensió de llurs propietats.En el capítol Models de densitats electròniques moleculars es presenten procediments computacionals originals per l'ajust de funcions densitat a models expandits en termes de gaussianes 1s centrades en els nuclis. Les restriccions físico-matemàtiques associades a les distribucions de probabilitat s'introdueixen de manera rigorosa, en el procediment anomenat Atomic Shell Approximation (ASA). Aquest procediment, implementat en el programa ASAC, parteix d'un espai funcional quasi complert, d'on se seleccionen variacionalment les funcions o capes de l'expansió, d'acord als requisits de no negativitat. La qualitat d'aquestes densitats i de les mesures de semblança derivades es verifica abastament. Aquest model ASA s'estén a representacions dinàmiques, físicament més acurades, en quant que afectades per les vibracions nuclears, cara a una exploració de l'efecte de l'esmorteïment dels pics nuclears en les mesures de semblança molecular. La comparació de les densitats dinàmiques respecte les estàtiques evidencia un reordenament en les densitats dinàmiques, d'acord al que constituiria una manifestació del Principi quàntic de Le Chatelier. El procediment ASA, explícitament consistent amb les condicions de N-representabilitat, s'aplica també a la determinació directe de densitats electròniques hidrogenoides, en un context de teoria del funcional de la densitat.El capítol Maximització global de la funció de semblança presenta algorismes originals per la determinació de la màxima sobreposició de les densitats electròniques moleculars. Les mesures de semblança molecular quàntica s'identifiquen amb el màxim solapament, de manera es mesuri la distància entre les molècules, independentment dels sistemes de referència on es defineixen les densitats electròniques. Partint de la solució global en el límit de densitats infinitament compactades en els nuclis, es proposen tres nivells de aproximació per l'exploració sistemàtica, no estocàstica, de la funció de semblança, possibilitant la identificació eficient del màxim global, així com també dels diferents màxims locals. Es proposa també una parametrització original de les integrals de recobriment a través d'ajustos a funcions lorentzianes, en quant que tècnica d'acceleració computacional. En la pràctica de les relacions estructura-activitat, aquests avenços possibiliten la implementació eficient de mesures de semblança quantitatives, i, paral·lelament, proporcionen una metodologia totalment automàtica d'alineació molecular. El capítol Semblances d'àtoms en molècules descriu un algorisme de comparació dels àtoms de Bader, o regions tridimensionals delimitades per superfícies de flux zero de la funció de densitat electrònica. El caràcter quantitatiu d'aquestes semblances possibilita la mesura rigorosa de la noció química de transferibilitat d'àtoms i grups funcionals. Les superfícies de flux zero i els algorismes d'integració usats han estat publicats recentment i constitueixen l'aproximació més acurada pel càlcul de les propietats atòmiques. Finalment, en el capítol Semblances en estructures cristal·lines hom proposa una definició original de semblança, específica per la comparació dels conceptes de suavitat o softness en la distribució de fonons associats a l'estructura cristal·lina. Aquests conceptes apareixen en estudis de superconductivitat a causa de la influència de les interaccions electró-fonó en les temperatures de transició a l'estat superconductor. En aplicar-se aquesta metodologia a l'anàlisi de sals de BEDT-TTF, s'evidencien correlacions estructurals entre sals superconductores i no superconductores, en consonància amb les hipòtesis apuntades a la literatura sobre la rellevància de determinades interaccions.Conclouen aquesta tesi un apèndix que conté el programa ASAC, implementació de l'algorisme ASA, i un capítol final amb referències bibliogràfiques.

A Field Evaluation of the Time-of-Detection Method to Estimate Population Size and Density for Aural Avian Point Counts

The time-of-detection method for aural avian point counts is a new method of estimating abundance, allowing for uncertain probability of detection. The method has been specifically designed to allow for variation in singing rates of birds. It involves dividing the time interval of the point count into several subintervals and recording the detection history of the subintervals when each bird sings. The method can be viewed as generating data equivalent to closed capture–recapture information. The method is different from the distance and multiple-observer methods in that it is not required that all the birds sing during the point count. As this method is new and there is some concern as to how well individual birds can be followed, we carried out a field test of the method using simulated known populations of singing birds, using a laptop computer to send signals to audio stations distributed around a point. The system mimics actual aural avian point counts, but also allows us to know the size and spatial distribution of the populations we are sampling. Fifty 8-min point counts (broken into four 2-min intervals) using eight species of birds were simulated. Singing rate of an individual bird of a species was simulated following a Markovian process (singing bouts followed by periods of silence), which we felt was more realistic than a truly random process. The main emphasis of our paper is to compare results from species singing at (high and low) homogenous rates per interval with those singing at (high and low) heterogeneous rates. Population size was estimated accurately for the species simulated, with a high homogeneous probability of singing. Populations of simulated species with lower but homogeneous singing probabilities were somewhat underestimated. Populations of species simulated with heterogeneous singing probabilities were substantially underestimated. Underestimation was caused by both the very low detection probabilities of all distant individuals and by individuals with low singing rates also having very low detection probabilities.

Understanding mixing efficiency in the oceans. Do the nonlinearities of the equation of state matter?

There exist two central measures of turbulent mixing in turbulent stratified fluids that are both caused by molecular diffusion: 1) the dissipation rate D(APE) of available potential energy APE; 2) the turbulent rate of change Wr, turbulent of background gravitational potential energy GPEr. So far, these two quantities have often been regarded as the same energy conversion, namely the irreversible conversion of APE into GPEr, owing to the well known exact equality D(APE)=Wr, turbulent for a Boussinesq fluid with a linear equation of state. Recently, however, Tailleux (2009) pointed out that the above equality no longer holds for a thermally-stratified compressible, with the ratio ξ=Wr, turbulent/D(APE) being generally lower than unity and sometimes even negative for water or seawater, and argued that D(APE) and Wr, turbulent actually represent two distinct types of energy conversion, respectively the dissipation of APE into one particular subcomponent of internal energy called the "dead" internal energy IE0, and the conversion between GPEr and a different subcomponent of internal energy called "exergy" IEexergy. In this paper, the behaviour of the ratio ξ is examined for different stratifications having all the same buoyancy frequency N vertical profile, but different vertical profiles of the parameter Υ=α P/(ρCp), where α is the thermal expansion coefficient, P the hydrostatic pressure, ρ the density, and Cp the specific heat capacity at constant pressure, the equation of state being that for seawater for different particular constant values of salinity. It is found that ξ and Wr, turbulent depend critically on the sign and magnitude of dΥ/dz, in contrast with D(APE), which appears largely unaffected by the latter. These results have important consequences for how the mixing efficiency should be defined and measured in practice, which are discussed.

Suprathermal electron evolution in a Parker spiral magnetic field

Suprathermal electrons (>70 eV) form a small fraction of the total solar wind electron density but serve as valuable tracers of heliospheric magnetic field topology. Their usefulness as tracers of magnetic loops with both feet rooted on the Sun, however, most likely fades as the loops expand beyond some distance owing to scattering. As a first step toward quantifying that distance, we construct an observationally constrained model for the evolution of the suprathermal electron pitch-angle distributions on open field lines. We begin with a near-Sun isotropic distribution moving antisunward along a Parker spiral magnetic field while conserving magnetic moment, resulting in a field-aligned strahl within a few solar radii. Past this point, the distribution undergoes little evolution with heliocentric distance. We then add constant (with heliocentric distance, energy, and pitch angle) ad-hoc pitch-angle scattering. Close to the Sun, pitch-angle focusing still dominates, again resulting in a narrow strahl. Farther from the Sun, however, pitch-angle scattering dominates because focusing is effectively weakened by the increasing angle between the magnetic field direction and intensity gradient, a result of the spiral field. We determine the amount of scattering required to match Ulysses observations of strahl width in the fast solar wind, providing an important tool for inferring the large-scale properties and topologies of field lines in the interplanetary medium. Although the pitch-angle scattering term is independent of energy, time-of-flight effects in the spiral geometry result in an energy dependence of the strahl width that is in the observed sense although weaker in magnitude.

Understanding electron heat flux signatures in the solar wind

Suprathermal electrons (E > 80 eV) carry heat flux away from the Sun. Processes controlling the heat flux are not well understood. To gain insight into these processes, we model heat flux as a linear dependence on two independent parameters: electron number flux and electron pitch angle anisotropy. Pitch angle anisotropy is further modeled as a linear dependence on two solar wind components: magnetic field strength and plasma density. These components show no correlation with number flux, reinforcing its independence from pitch angle anisotropy. Multiple linear regression applied to 2 years of Wind data shows good correspondence between modeled and observed heat flux and anisotropy. The results suggest that the interplay of solar wind parameters and electron number flux results in distinctive heat flux dropouts at heliospheric features like plasma sheets but that these parameters continuously modify heat flux. This is inconsistent with magnetic disconnection as the primary cause of heat flux dropouts. Analysis of fast and slow solar wind regimes separately shows that electron number flux and pitch angle anisotropy are equally correlated with heat flux in slow wind but that number flux is the dominant correlative in fast wind. Also, magnetic field strength correlates better with pitch angle anisotropy in slow wind than in fast wind. The energy dependence of the model fits suggests different scattering processes in fast and slow wind.

Ultrafast excited state dynamics controlling photochemical isomerization of N-methyl-4-[trans-2-(4-pyridyl)ethenyl]pyridinium coordinated to a {Re-1(CO)(3)(2,2 '-bipyridine)} chromophore

Two Multifunctional photoactive complexes [Re(Cl)(CO)(3)-(MeDpe(+))(2)](2+) and [Re(MeDpe(+))(CO)(3)(bpy)](2+) (MeDpe(+) = N-methyl-4-[trans-2-(4-pyridyl)ethenyl]pyridinium, bpy = 2,2'-bipyridine) were synthesized. characterized. and their redox and photonic properties were investigated by cyclic voltammetry: ultraviolet-visible-infrared (UV/Vis/IR) spectroelectrochemistry, stationary UV/Vis and resonance Raman spectroscopy; photolysis; picosecond time-resolved absorption spectroscopy in the visible and infrared regions: and time-resolved resonance Raman spectroscopy. The first reduction step of either complex Occurs at about -1.1 V versus Fc/Fc(+) and is localized at MeDpe(+). Reduction alone does not induce a trans -> cis isomerization of MeDpe(+). [Re(Cl)(CO)(3)(MeDPe(+))(2)](2+) is photostable, while [Re(MeDpe(+))(CO)(3)(bpy)](2+) and free MeDpe(+) isomerize under near-UV irradiation. The lowest excited state of [Re(Cl)(CO)(3)(MeDPe(+))(2)](2+) has been identified as the Re(Cl)(CO)(3) -> MeDpe(+) (MLCT)-M-3 (MLCT = metal-to-ligand charge transfer), decaying directly to the ground state with lifetimes of approximate to 42 (73%) and approximate to 430ps (27%). Optical excitation of [Re(MeDpe(+))(CO)(3)(bpy)](2+) leads to population of Re(CO)(3) -> MeDpe(+) and Re(CO)(3) -> bpy (MLCT)-M-3 states, from which a MeDpe(+) localized intraligand 3 pi pi* excited state ((IL)-I-3) is populated with lifetimes of approximate to 0.6 and approximate to 10 ps, respectively. The 3IL state undergoes a approximate to 21 ps internal rotation, which eventually produces the cis isomer on a much longer timescale. The different excited-state behavior of the two complexes and the absence of thermodynamically favorable interligand electron transfer in excited [Re(MeDpe(+))(CO)(3)(bpy)](2+) reflect the fine energetic balance between excited states of different orbital origin, which can be tuned by subtle Structural variations. The complex [Re(MeDpe+)(CO)(3)(bpy)](2+) emerges as a prototypical, multifunctional species with complementary redox and photonic behavior.

beta-Sheet mediated self-assembly of dipeptides of omega-amino acids and remarkable fibrillation in the solid state

Single crystal X-ray diffraction studies show that the extended structure of dipeptide I Boc-beta-Ala-m-ABA-OMe (m-ABA: meta-aminobenzoic acid) self-assembles in the solid state by intermolecular hydrogen bonding to create an infinite parallel P-sheet structure. In dipeptide II Boc-gamma-Abu-m-ABA-OMe (gamma-Abu: gamma-aminobutyric acid), two such parallel beta-sheets are further cross-linked by intermolecular hydrogen bonding through m-aminobenzoic acid moieties. SEM (scanning electron microscopy) studies reveal that both the peptides I and II form amyloid-like fibrils in the solid state. The fibrils are also found to be stained readily by Congo red, a characteristic feature of the amyloid fiber whose accumulation causes several fatal diseases such as Alzheimer's, prion-protein etc.

Supramolecular helix and beta-sheet through self-assembly of two isomeric tetrapeptides in crystals and formation of filaments and ribbons in the solid state

Single crystal X-ray diffraction studies show that the beta-turn structure of tetrapeptide I, Boc-Gly-Phe-Aib-Leu-OMe (Aib: alpha-amino isobutyric acid) self-assembles to a supramolecular helix through intermolecular hydrogen bonding along the crystallographic a axis. By contrast the beta-turn structure of an isomeric tetrapeptide II, Boc-Gly-Leu-Aib-Phe-OMe self-assembles to a supramolecular beta-sheet-like structure via a two-dimensional (a, b axis) intermolecular hydrogen bonding network and pi-pi interactions. FT-IR studies of the peptides revealed that both of them form intermolecularly hydrogen bonded supramolecular structures in the solid state. Field emission scanning electron micrographs (FE-SEM) of the dried fibrous materials of the peptides show different morphologies, non-twisted filaments in case of peptide I and non-twisted filaments and ribbon-like structures in case of peptide II.

A pulse radiolysis study of free radicals formed by one-electron oxidation of the antimalarial drug pyronaridine

Free radicals from one-electron oxidation of the antimalarial drug pyronaridine have been studied by pulse radiolysis. The results show that pyronaridine is readily oxidised to an intermediate semi-iminoquine radical by inorganic and organic free radicals, including those derived from tryptophan and acetaminophen. The pyronaridine radical is rapidly reduced by both ascorbate and caffeic acid. The results indicate that the one-electron reduction potential of the pyronaridine radical at neutral pH lies between those of acetaminophen (707 mV) and caffeic acid (534 mV). The pyronaridine radical decays to produce the iminoquinone, detected by electrospray mass spectrometry, in a second-order process that density functional theory (DFT) calculations (UB3LYP/6-31+G*) suggest is a disproportionation reaction. Important calculated dimensions of pyronaridine, its phenoxyl and aminyl radical, as well as the iminoquinone, are presented.

Self-assembly of beta-turn forming synthetic tripeptides into supramolecular beta-sheets and amyloid-like fibrils in the solid state

We have described here the self-assembling properties of the synthetic tripeptides Boc-Ala(1)-Aib(2) -Val (3)-OMe 1, BocAla(l)-Aib(2)-Ile(3)-OMe 2 and Boc-Ala(l)-Gly(2)-Val(3)-OMe 3 (Aib=alpha-arnino isobutyric acid, beta-Ala=beta-alanine) which have distorted beta-turn conformations in their respective crystals. These turn-forming tripeptides self-assemble to form supramolecular beta-sheet structures through intermolecular hydrogen bonding and other noncovalent interactions. The scanning electron micrographs of these peptides revealed that these compounds form amyloid-like fibrils, the causative factor for many neurodegenerative diseases including Alzheimer's disease, Huntington's disease and Prion-related encephalopathies. (C) 2004 Elsevier Ltd. All rights reserved.