On the absorbance changes in the photocycle of the photoactive yellow protein: A quantum-chemical analysis

Spectral changes in the photocycle of the photoactive yellow protein (PYP) are investigated by using ab initio multiconfigurational second-order perturbation theory at the available structures experimentally determined. Using the dark ground-state crystal structure [Genick, U. K., Soltis, S. M., Kuhn, P., Canestrelli, I. L. & Getzoff, E. D. (1998) Nature (London) 392, 206–209], the ππ* transition to the lowest excited state is related to the typical blue-light absorption observed at 446 nm. The different nature of the second excited state (nπ*) is consistent with the alternative route detected at 395-nm excitation. The results suggest the low-temperature photoproduct PYPHL as the most plausible candidate for the assignment of the cryogenically trapped early intermediate (Genick et al.). We cannot establish, however, a successful correspondence between the theoretical spectrum for the nanosecond time-resolved x-ray structure [Perman, B., Šrajer, V., Ren, Z., Teng, T., Pradervand, C., et al. (1998) Science 279, 1946–1950] and any of the spectroscopic photoproducts known up to date. It is fully confirmed that the colorless light-activated intermediate recorded by millisecond time-resolved crystallography [Genick, U. K., Borgstahl, G. E. O., Ng, K., Ren, Z., Pradervand, C., et al. (1997) Science 275, 1471–1475] is protonated, nicely matching the spectroscopic features of the photoproduct PYPM. The overall contribution demonstrates that a combined analysis of high-level theoretical results and experimental data can be of great value to perform assignments of detected intermediates in a photocycle.

An approach to three-dimensional structures of biomolecules by using single-molecule diffraction images

We describe an approach to the high-resolution three-dimensional structural determination of macromolecules that utilizes ultrashort, intense x-ray pulses to record diffraction data in combination with direct phase retrieval by the oversampling technique. It is shown that a simulated molecular diffraction pattern at 2.5-Å resolution accumulated from multiple copies of single rubisco biomolecules, each generated by a femtosecond-level x-ray free electron laser pulse, can be successfully phased and transformed into an accurate electron density map comparable to that obtained by more conventional methods. The phase problem is solved by using an iterative algorithm with a random phase set as an initial input. The convergence speed of the algorithm is reasonably fast, typically around a few hundred iterations. This approach and phasing method do not require any ab initio information about the molecule, do not require an extended ordered lattice array, and can tolerate high noise and some missing intensity data at the center of the diffraction pattern. With the prospects of the x-ray free electron lasers, this approach could provide a major new opportunity for the high-resolution three-dimensional structure determination of single biomolecules.

Coupling the folding of homologous proteins

The empirical observation that homologous proteins fold to similar structures is used to enhance the capabilities of an ab initio algorithm to predict protein conformations. A penalty function that forces homologous proteins to look alike is added to the potential and is employed in the coupled energy optimization of several homologous proteins. Significant improvement in the quality of the computed structures (as compared with the computational folding of a single protein) is demonstrated and discussed.

Indium-cadmium-oxide films having exceptional electrical conductivity and optical transparency: Clues for optimizing transparent conductors

Materials with high electrical conductivity and optical transparency are needed for future flat panel display, solar energy, and other opto-electronic technologies. InxCd1-xO films having a simple cubic microstructure have been grown on amorphous glass substrates by a straightforward chemical vapor deposition process. The x = 0.05 film conductivity of 17,000 S/cm, carrier mobility of 70 cm2/Vs, and visible region optical transparency window considerably exceed the corresponding parameters for commercial indium-tin oxide. Ab initio electronic structure calculations reveal small conduction electron effective masses, a dramatic shift of the CdO band gap with doping, and a conduction band hybridization gap caused by extensive Cd 5s + In 5s mixing.

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Proactive and reactive inhibition during overt and covert actions. An electrical neuroimaging study.

Response inhibition is the ability to suppress inadequate but automatically activated, prepotent or ongoing response tendencies. In the framework of motor inhibition, two distinct operating strategies have been described: “proactive” and “reactive” control modes. In the proactive modality, inhibition is recruited in advance by predictive signals, and actively maintained before its enactment. Conversely, in the reactive control mode, inhibition is phasically enacted after the detection of the inhibitory signal. To date, ample evidence points to a core cerebral network for reactive inhibition comprising the right inferior frontal gyrus (rIFG), the presupplementary motor area (pre-SMA) and the basal ganglia (BG). Moreover, fMRI studies showed that cerebral activations during proactive and reactive inhibition largely overlap. These findings suggest that at least part of the neural network for reactive inhibition is recruited in advance, priming cortical regions in preparation for the upcoming inhibition. So far, proactive and reactive inhibitory mechanisms have been investigated during tasks in which the requested response to be stopped or withheld was an “overt” action execution (AE) (i.e., a movement effectively performed). Nevertheless, inhibitory mechanisms are also relevant for motor control during “covert actions” (i.e., potential motor acts not overtly performed), such as motor imagery (MI). MI is the conscious, voluntary mental rehearsal of action representations without any overt movement. Previous studies revealed a substantial overlap of activated motor-related brain networks in premotor, parietal and subcortical regions during overtly executed and imagined movements. Notwithstanding this evidence for a shared set of cerebral regions involved in encoding actions, whether or not those actions are effectively executed, the neural bases of motor inhibition during MI, preventing covert action from being overtly performed, in spite of the activation of the motor system, remain to be fully clarified. Taking into account this background, we performed a high density EEG study evaluating cerebral mechanisms and their related sources elicited during two types of cued Go/NoGo task, requiring the execution or withholding of an overt (Go) or a covert (MI) action, respectively. The EEG analyses were performed in two steps, with different aims: 1) Analysis of the “response phase” of the cued overt and covert Go/NoGo tasks, for the evaluation of reactive inhibitory control of overt and covert actions. 2) Analysis of the “preparatory phase” of the cued overt and covert Go/NoGo EEG datasets, focusing on cerebral activities time-locked to the preparatory signals, for the evaluation of proactive inhibitory mechanisms and their related neural sources. For these purposes, a spatiotemporal analysis of the scalp electric fields was applied on the EEG data recorded during the overt and covert Go/NoGo tasks. The spatiotemporal approach provide an objective definition of time windows for source analysis, relying on the statistical proof that the electric fields are different and thus generated by different neural sources. The analysis of the “response phase” revealed that key nodes of the inhibitory circuit, underpinning inhibition of the overt movement during the NoGo response, were also activated during the MI enactment. In both cases, inhibition relied on the activation of pre-SMA and rIFG, but with different temporal patterns of activation in accord with the intended “covert” or “overt” modality of motor performance. During the NoGo condition, the pre-SMA and rIFG were sequentially activated, pointing to an early decisional role of pre-SMA and to a later role of rIFG in the enactment of inhibitory control of the overt action. Conversely, a concomitant activation of pre-SMA and rIFG emerged during the imagined motor response. This latter finding suggested that an inhibitory mechanism (likely underpinned by the rIFG), could be prewired into a prepared “covert modality” of motor response, as an intrinsic component of the MI enactment. This mechanism would allow the rehearsal of the imagined motor representations, without any overt movement. The analyses of the “preparatory phase”, confirmed in both overt and covert Go/NoGo tasks the priming of cerebral regions pertaining to putative inhibitory network, reactively triggered in the following response phase. Nonetheless, differences in the preparatory strategies between the two tasks emerged, depending on the intended “overt” or “covert” modality of the possible incoming motor response. During the preparation of the overt Go/NoGo task, the cue primed the possible overt response programs in motor and premotor cortex. At the same time, through preactivation of a pre-SMA-related decisional mechanism, it triggered a parallel preparation for the successful response selection and/or inhibition during the subsequent response phase. Conversely, the preparatory strategy for the covert Go/NoGo task was centred on the goal-oriented priming of an inhibitory mechanism related to the rIFG that, being tuned to the instructed covert modality of the motor performance and instantiated during the subsequent MI enactment, allowed the imagined response to remain a potential motor act. Taken together, the results of the present study demonstrate a substantial overlap of cerebral networks activated during proactive recruitment and subsequent reactive enactment of motor inhibition in both overt and covert actions. At the same time, our data show that preparatory cues predisposed ab initio a different organization of the cerebral areas (in particular of the pre-SMA and rIFG) involved with sensorimotor transformations and motor inhibitory control for executed and imagined actions. During the preparatory phases of our cued overt and covert Go/NoGo tasks, the different adopted strategies were tuned to the “how” of the motor performance, reflecting the intended overt and covert modality of the possible incoming action.

Análise Conformacional e estudo das interações eletrônicas de algumas α-fenilseleno-α-dietóxifosforilacetofenonas para-substituídas

A presente Dissertação relata a síntese e o estudo conformacional das α-fenilseleno-α-dietóxifosforilacetofenonas para-substituídas p-X-Φ-C(O)CH[SeΦ][P(O)(OEt2] (X=OMe 1, Me 2, H 3, F 4, Cl 5, Br 6 e NO2 7) através da banda de estiramento da carbonila no infravermelho, em solventes de polaridade crescente apoiado por cálculos ab initio HF/6-3IG**. A comparação entre a freqüência e a intensidade relativa dos componentes do dubleto, para os derivados 6 e 7, e do singleto para os derivados 1-5, no solvente apolar tetracloreto de carbono, e dos componentes do dubleto, nos solventes de polaridade crescente (clorofórmio, diclorometano e acetonitrila), para os derivados 1-7, com os dados do cálculo ab initio de 3 (composto de referência), indicou que ambas as conformações estáveis (g1 e g2) apresentam a ligação C-Se na geometria anti-clinal (gauche) em relação à carbonila (C=O), enquanto que a ligação C-P assume uma geometria sin-periplanar (cis) em relação à carbonila. A análise dos contatos interatômicos de átomos relevante em comparação com a soma de seus raios de van der Waals, indicou que ambas as conformações g1 e g2 são fortemente estabilizadas pelo sinergismo das interações orbitalares e eletrostáticas π*(CO) / nSe e Oδ-[CO].....Pδ+[PO]. Analogamente, as interações mais fracas Oδ-[OR]..... Cδ+[CO], 0-Hδ+[SeΦ]....Oδ-[PO] e 0-Hδ+[ΦC(O)]....Oδ-[CO] estabilizam as conformações g1 e g2, aproximadamente na mesma extensão. No entanto, somente a conformação g1 é estabilizada pela interação eletrostática (ligação de hidrogênio) Hδ+[α-CH].....Oδ-[OR], enquanto que sómente a conformação g2 é desestabilizada pelo Efeito de Campo Repulsivo entre os dipolos Cδ+=.Oδ- e Pδ+-ORδ- Assim sendo, pode-se concluir que no dubleto de VCO no IV, o componente de maior freqüência e de menor intensidade corresponde à conformação menos estável g2 (do cálculo) enquanto que o componente de menor freqüência e mais intenso corresponde à conformação mais estável g1 (do cálculo). Estes dados estão de pleno acordo com os deslocamentos de freqüência mais negativos da carbonila (ΔVCO) do confôrmero mais estável g1 em relação ao menos estável g2.

Estudo da cristalinidade de filmes finos de nitreto de índio e simulado pelo pacote de programas Wien2k

Neste trabalho, foi utilizado o método de deposição assistida por feixe de íons (IBAD na sigla em inglês) para produção de filmes finos de nitreto de índio em substratos de silício (111) e Safira-C. Variando as condições de deposição e utlilizando a técnica de difração de raios-X, investigou-se com o intuito de obter os parâmetros que resultam em filmes finos com melhor grau de cristalinidade. Os filmes produzidos a 380C apresentaram alta cristalinidade, superior àqueles a 250C. Temperaturas muito superiores a 380C não ocasionam a formação de filme cristalino de InN, como foi observado ao utilizar a temperatura de 480C; o mesmo se observa ao utilizar temperatura ambiente. Na temperatura considerada adequada ,de 380C, obteve-se que a utilização de Ra, ou seja, a razão de fluxo de partículas entre o nitrogênio e índio, em torno de 2,3 permite obter um melhor grau de cristalinização, o qual decresce conforme se diverge desse valor. A comparação entre difratogramas de amostras produzidas com e sem a evaporação prévia de titânio, o qual é possível observar um deslocamento dos picos do InN, indicam que o efeito Gettering permite a redução de impurezas no filme, principalmente de oxigênio. Utilizou-se a técnica de Retroespalhamento de Rutherford para obtenção da composição dos elementos e o perfil de profundidade. Notou-se uma forte mistura dos elementos do substrato de silício e safira com o nitreto de índio mesmo próximos a superfície. A presença indesejável de impurezas, principalmente o oxigênio, durante a deposição de filmes finos é praticamente inevitável. Desta forma, cálculos ab initio baseados na Teoria do Funcional da Densidade (DFT) foram realizados para investigar defeitos isolados e complexos de oxigênio no nitreto de índio e a sua influência nas propriedades óticas. Considerou-se diferentes concentrações de oxigênio (x=2,76, 8,32, 11,11 e 22,22%) aplicando-se o método PBEsolGGA e TB-mBJ para o tratamento da energia e potencial de troca e correlação. Obteve-se que é energeticamente favorável o oxigênio existir principalmente como defeito carregado e isolado. Os resultados utilizando a aproximação de TB-mBJ indicam um estreitamento do bandgap conforme a concentração de oxigênio aumenta. Entretanto, a alta contribuição do efeito de Moss-Burstein resulta num efetivo alargamento do band gap, gerando valores de band gap ótico maiores que no do bulk de nitreto de índio.

Mechanical, electrical, and magnetic properties of Ni nanocontacts

The dynamic deformation upon stretching of Ni nanowires as those formed with mechanically controllable break junctions or with a scanning tunneling microscope is studied both experimentally and theoretically. Molecular dynamics simulations of the breaking process are performed. In addition, and in order to compare with experiments, we also compute the transport properties in the last stages before failure using the first-principles implementation of Landauer's formalism included in our transport package ALACANT.

Magnetic and orbital blocking in Ni nanocontacts

We address the fundamental question of whether magnetoresistance (MR) of atomic-sized contacts of nickel is very large because of the formation of a domain wall (DW) at the neck. Using ab initio transport calculations we find that, as in the case of nonmagnetic electrodes, transport in Ni nanocontacts depends very much on the orbital nature of the electrons. Our results are in agreement with several experiments in the average value of the conductance. On the other hand, contrary to existing claims, DW scattering does not account for large MR in Ni nanocontacts.

Anisotropic magnetoresistance in nanocontacts

We present ab initio calculations of the evolution of anisotropic magnetoresistance (AMR) in Ni nanocontacts from the ballistic to the tunnel regime. We find an extraordinary enhancement of AMR, compared to bulk, in two scenarios. In systems without localized states, such as chemically pure break junctions, large AMR only occurs if the orbital polarization of the current is large, regardless of the anisotropy of the density of states. In systems that display localized states close to the Fermi energy, such as a single electron transistor with ferromagnetic electrodes, large AMR is related to the variation of the Fermi energy as a function of the magnetization direction.

Electronic structure and transport properties of atomic NiO spinvalves

Ab initio quantum transport calculations show that short NiO chains suspended in Ni nanocontacts present a very strong spin-polarization of the conductance.The generalized gradient approximation we use here predicts a similar polarization of the conductance as the one previously computed with non-local exchange, confirming the robustness of the result. Their use as nanoscopic spinvalves is proposed.

Spin alignment of extra electrons in K-phenanthrene clusters taken from the crystalline tripotassium-intercalated phenanthrene structure

The appearance of ferromagnetic correlations among π electrons of phenanthrene (C14H10) molecules in the herringbone structure is proven for K doped clusters both by ab initio quantum-chemistry calculations and by the direct solution of the many-body Pariser-Parr-Pople Hamiltonian. Magnetic ground states are predicted for one or three additional electrons per phenanthrene molecule. These results are a consequence of the small overlap between the lowest unoccupied molecular orbitals (and lowest unoccupied molecular orbitals + 1) of neutral neighboring phenanthrene molecules, which makes the gain in energy by delocalization similar to the corresponding increase due to the Coulomb interaction.

Understanding the structure of the first atomic contact in gold

We have studied experimentally jump-to-contact (JC) and jump-out-of-contact (JOC) phenomena in gold electrodes. JC can be observed at first contact when two metals approach each other, while JOC occurs in the last contact before breaking. When the indentation depth between the electrodes is limited to a certain value of conductance, a highly reproducible behaviour in the evolution of the conductance can be obtained for hundreds of cycles of formation and rupture. Molecular dynamics simulations of this process show how the two metallic electrodes are shaped into tips of a well-defined crystallographic structure formed through a mechanical annealing mechanism. We report a detailed analysis of the atomic configurations obtained before contact and rupture of these stable structures and obtained their conductance using first-principles quantum transport calculations. These results help us understand the values of conductance obtained experimentally in the JC and JOC phenomena and improve our understanding of atomic-sized contacts and the evolution of their structural characteristics.

Exponential decay of spin-spin correlation between distant defect states produced by contour hydrogenation of polycyclic aromatic hydrocarbon molecules

The first few low-lying spin states of alternant polycyclic aromatic hydrocarbon (PAH) molecules of several shapes showing defect states induced by contour hydrogenation have been studied both by ab initio methods and by a precise numerical solution of Pariser-Parr-Pople (PPP) interacting model. In accordance with Lieb's theorem, the ground state shows a spin multiplicity equal to one for balanced molecules, and it gets larger values for imbalanced molecules (that is, when the number of π electrons on both subsets is not equal). Furthermore, we find a systematic decrease of the singlet-triplet splitting as a function of the distance between defects, regardless of whether the ground state is singlet or triplet. For example, a splitting smaller than 0.001 eV is obtained for a medium size C46H28 PAH molecule (di-hydrogenated [11]phenacene) showing a singlet ground state. We conclude that π electrons unbound by lattice defects tend to remain localized and unpaired even when long-range Coulomb interaction is taken into account. Therefore they show a biradical character (polyradical character for more than two defects) and should be studied as two or more local doublets. The implications for electron transport are potentially important since these unpaired electrons can trap traveling electrons or simply flip their spin at a very small energy cost.