Site-specific conformational determination in thermal unfolding studies of helical peptides using vibrational circular dichroism with isotopic substitution

Understanding the detailed mechanism of protein folding requires dynamic, site-specific stereochemical information. The short time response of vibrational spectroscopies allows evaluation of the distribution of populations in rapid equilibrium as the peptide unfolds. Spectral shifts associated with isotopic labels along with local stereochemical sensitivity of vibrational circular dichroism (VCD) allow determination of the segment sequence of unfolding. For a series of alanine-rich peptides that form α-helices in aqueous solution, we used isotopic labeling and VCD to demonstrate that the α-helix noncooperatively unwinds from the ends with increasing temperature. For these blocked peptides, the C-terminal is frayed at 5°C. Ab initio level theoretical simulations of the IR and VCD band shapes are used to analyze the spectra and to confirm the conformation of the labeled components. The VCD signals associated with the labeled residues are amplified by coupling to the nonlabeled parts of the molecule. Thus small labeled segments are detectable and stereochemically defined in moderately large peptides in this report of site-specific peptide VCD conformational analysis.

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.

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.

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.

Theoretical insights on electron donor-acceptor interactions involving carbon dioxide

Electron donor-acceptor (EDA) interactions are widely involved in chemistry and their understanding is essential to design new technological applications in a variety of fields ranging from material sciences and chemical engineering to medicine. In this work, we study EDA complexes of carbon dioxide with ketones using several ab initio and Density Functional Theory methods. Energy contributions to the interaction energy have been analyzed in detail using both variational and perturbational treatments. Dispersion energy has been shown to play a key role in explaining the high stability of a non-conventional structure, which can roughly be described by a cooperative EDA interaction.

Towards Accurate and Efficient Description of Excited States

Thesis (Ph.D.)--University of Washington, 2016-06

Electronic structure methods applied to gas-carbon reactions

A review is given on the fundamental studies of gas-carbon reactions using electronic structure methods in the last several decades. The three types of electronic structure methods including semi-empirical, ab initio and density functional theory, methods are briefly introduced first, followed by the studies on carbon reactions with hydrogen and oxygen-containing gases (non-catalysed and catalysed). The problems yet to solve and possible promising directions are discussed. (C) 2002 Elsevier Science Ltd. All rights reserved.

New insights into NO-carbon and N2O-carbon reactions from quantum mechanical calculations

Density functional theory calculations were used to investigate the mechanisms of NO-carbon and N2O-carbon reactions. It was the first time that the importance of surface nitrogen groups was addressed in the kinetic behaviors of the NO-carbon reaction. It was found that the off-plane nitrogen groups that are adjacent to the zigzag edge sites and in-plane nitrogen groups that are located on the armchair sites make the bond energy of oxygen desorption even ca. 20% lower than that of the off-plane epoxy group adjacent to zigzag edge sites and in-plane o-quinone oxygen atoms on armchair sites; this may explain the reason why the experimentally obtained activation energy of the NO-carbon reaction is ca. 20% lower than that of the O-2-carbon reaction over 923 K. A higher ratio of oxygen atoms can be formed in the N2O-carbon reaction, because of the lower dissociation energy of N2O, which results in a higher ratio of off-plane epoxy oxygen atoms. The desorption energy of semiquinone with double adjacent off-plane oxygen groups is ca. 20% less than that of semiquinone with only one adjacent off-plane oxygen group. This may be the reason why the activation energy of N2O is also ca. 20% less than that of the O-2-carbon reaction. The new mechanism can also provide a good qualitative comparison for the relative reaction rates of NO-, N2O-, and O-2-carbon reactions. The anisotropic characters of these gas-carbon reactions can also be well explained.

On the microscopic mechanism of carbon gasification: A theoretical study

In this paper we report the results of ab initio calculations on the energetics and kinetics of oxygen-driven carbon gasification reactions using a small model cluster, with full characterisation of the stationary points on the reaction paths. We show that previously unconsidered pathways present significantly reduced barriers to reaction and must be considered as alternative viable paths. At least two electronic spin states of the model cluster must be considered for a complete description. (C) 2004 Elsevier Ltd. All rights reserved.

The rearrangements of naphthyinitrenes: UV/Vis and IR spectra of azirines, cyclic ketenimines, and cyclic nitrile ylides

Ar matrix photolysis of 1- and 2-naphthyl azides 3 and 4 at 313 nm initially affords the singlet naphthyl nitrenes, (1)1 and (1)2. Relaxation to the corresponding lower energy, persistent triplet nitrenes (3)1 and (3)2 competes with cyclization to the azirines 15 and 18, which can also be formed photochemically from the triplet nitrenes. On prolonged irradiation, the azirines can be converted to the seven-membered cyclic ketenimines 10 and 13, respectively, as described earlier by Dunkin and Thomson. However, instead of the o-quinoid ketenimines 16 and 19, which are the expected primary ring-opening products of azirines 15 and 18, respectively, we observed their novel bond-shift isomers 17 and 20, which may be formally regarded as cyclic nitrile ylides. The existence of such ylidic heterocumulenes has been predicted previously, but this work provides the first experimental observation of such species. The factors which are responsible for the special stability of the ylidic species 17 and 20 are discussed.

Mg-based nanocomposites with high capacity and fast kinetics for hydrogen storage

Magnesium and its alloys have shown a great potential in effective hydrogen storage due to their advantages of high volumetric/ gravimetric hydrogen storage capacity and low cost. However, the use of these materials in fuel cells for automotive applications at the present time is limited by high hydrogenation temperature and sluggish sorption kinetics. This paper presents the recent results of design and development of magnesium-based nanocomposites demonstrating the catalytic effects of carbon nanotubes and transition metals on hydrogen adsorption in these materials. The results are promising for the application of magnesium materials for hydrogen storage, with significantly reduced absorption temperatures and enhanced ab/desorption kinetics. High level Density Functional Theory calculations support the analysis of the hydrogenation mechanisms by revealing the detailed atomic and molecular interactions that underpin the catalytic roles of incorporated carbon and titanium, providing clear guidance for further design and development of such materials with better hydrogen storage properties.

Oxoketene-oxoketene, imidoylketene-imidoylketene and oxoketenimine-imidoylketene rearrangements. 1,3-shifts of phenyl groups

Dibenzoylketene 5 undergoes degenerate 1,3-shifts of the phenyl group between acyl and ketene carbon atoms, thus interconverting it with 6 and 7. This 1,3-shift takes place in the gas phase under flash vacuum thermolysis (FVT) conditions, but not in solution at 110-145 degrees C. Imidoyl(benzoyl)ketene 13 undergoes degenerate 1,3-shift of the phenyl group on FVT, thus interconverting it with 14, but the ketenimine isomer 15 is not formed, and none of these shifts take place in the solid state at 250 degrees C. Imidoyl(p-toluoyl)ketene 21 undergoes a 1,3-p-tolyl shift, interconverting it with ketene 22 but not with ketenimine 23. The imidoyl(p-toluoyl)ketene rotamer 25 cyclizes to 4-toluoyloxyquinoline 28 and 4-quinolone 29. The cyclization of imidoyl(benzoyl)ketene 13 to 4-benzoyloxyquinoline 18, and of 25 to 28 involves 1,3-C-to-O shifts of benzoyl (toluoyl) groups. Calculations of the transition states for the transformations at the B3LYP/6-31G** level of theory are in agreement with the observed reaction preferences.

Strong electronic correlations in superconducting organic charge transfer salts

We review the role of strong electronic correlations in quasi-two-dimensional organic charge transfer salts such as (BEDT-TTF)(2)X, (BETS)(2)Y, and beta'-[Pd(dmit)(2)](2)Z. We begin by defining minimal models for these materials. It is necessary to identify two classes of material: the first class is strongly dimerized and is described by a half-filled Hubbard model; the second class is not strongly dimerized and is described by a quarter-filled extended Hubbard model. We argue that these models capture the essential physics of these materials. We explore the phase diagram of the half-filled quasi-two-dimensional organic charge transfer salts, focusing on the metallic and superconducting phases. We review work showing that the metallic phase, which has both Fermi liquid and 'bad metal' regimes, is described both quantitatively and qualitatively by dynamical mean field theory (DMFT). The phenomenology of the superconducting state is still a matter of contention. We critically review the experimental situation, focusing on the key experimental results that may distinguish between rival theories of superconductivity, particularly probes of the pairing symmetry and measurements of the superfluid stiffness. We then discuss some strongly correlated theories of superconductivity, in particular the resonating valence bond (RVB) theory of superconductivity. We conclude by discussing some of the major challenges currently facing the field. These include parameterizing minimal models, the evidence for a pseudogap from nuclear magnetic resonance (NMR) experiments, superconductors with low critical temperatures and extremely small superfluid stiffnesses, the possible spin- liquid states in kappa-(ET)(2)Cu-2(CN)(3) and beta'-[Pd(dmit)(2)](2)Z, and the need for high quality large single crystals.

Vibrational dynamics and structure of natural feldspars

The present study gives a contribution to the knowledge on the Na-feldspar and plagioclases, extending the database of the Raman spectra of plagioclases with different chemical compositions and structural orders. This information may be used for the future planetary explorations by “rovers”, for the investigation of ceramics nanocrystal materials and for the mineralogical phase identification in sediments. Na-feldspar and plagioclase solid solution have been investigated by Raman spectroscopy in order to determine the relationships between the vibrational changes and the plagioclase crystal chemistry and structure. We focused on the Raman micro-spectroscopy technique, being a non-destructive method, suited for contactless analysis with high spatial resolution. Chemical and structural analyses have been performed on natural samples to test the usefulness of Raman spectroscopy as a tool in the study of the pressure-induced structural deformations, the disordering processes due to change in the Al-Si distribution in the tetrahedral sites and, finally, in the determination of the anorthitic content (Anx) in plagioclase minerals. All the predicted 39 Ag Raman active modes have been identified and assigned to specific patterns of atomic vibrational motion. A detailed comparison between experimental and computed Raman spectra has been performed and previous assignments have been revised, solving some discrepancies reported in recent literature. The ab initio calculation at the hybrid HF/DFT level with the WC1LYP Hamiltonian has proven to give excellent agreement between calculated and experimentally measured Raman wavenumbers and intensities in triclinic minerals. A short digression on the 36 infrared active modes of Na-feldspar has been done too. The identification of all 39 computed Raman modes in the experimentally measured spectra of the fully ordered Na-feldspar, known as low albite, along with the detailed description of each vibrational mode, has been essential to extend the comparative analysis to the high pressure and high temperature structural forms of albite, which reflect the physical–chemical conditions of the hosting rocks. The understanding of feldspar structure response to pressure and temperature is crucial in order to constrain crustal behaviour. The compressional behaviour of the Na-feldspar has been investigated for the first time by Raman spectroscopy. The absence of phase transitions and the occurrence of two secondary compression mechanisms acting at different pressures have been confirmed. Moreover, Raman data suggest that the internal structural changes are confined to a small pressure interval, localized around 6 GPa, not spread out from 4 to 8 GPa as suggested by previous X-rays studies on elasticity. The dominant compression mechanisms act via tetrahedral tilting, while the T-O bond lengths remain nearly constant at moderate compressional regimes. At the spectroscopic level, this leads to the strong pressure dependencies of T-O-T bending modes, as found for the four modes at 478, 508, 578 and 815 cm-1. The Al-Si distribution in the tetrahedral sites affects also the Raman spectrum of Na-feldspar. In particular, peak broadening is more sensitive than peak position to changes in the degree of order. Raman spectroscopy is found to be a good probe for local ordering, in particular being sensitive to the first annealing steps, when the macroscopic order parameter is still high. Even though Raman data are scattered and there are outliers in the estimated values of the degree of order, the average peak linewidths of the Na-feldspar characteristic doublet band, labelled here as υa and υb, as a function of the order parameter Qod show interesting trends: both peak linewidths linearly increase until saturation. From Qod values lower than 0.6, peak broadening is no more affected by the Al-Si distribution. Moreover, the disordering process is found to be heterogeneous. SC-XRD and Raman data have suggested an inter-crystalline inhomogeneity of the samples, i.e., the presence of regions with different defect density on the micrometric scale. Finally, the influence of Ca-Na substitution in the plagioclase Raman spectra has been investigated. Raman spectra have been collected on a series of well characterized natural, low structural plagioclases. The variations of the Raman modes as a function of the chemical composition and the structural order have been determined. The number of the observed Raman bands at each composition gives information about the unit-cell symmetry: moving away from the C1 structures, the number of the Raman bands enhances, as the number of formula units in the unit cell increases. The modification from an “albite-like” Raman spectrum to a more “anorthite-like” spectrum occurs from sample An78 onwards, which coincides with the appearance of c reflections in the diffraction patterns of the samples. The evolution of the Raman bands υa and υb displays two changes in slope at ~An45 and ~An75: the first one occurs between e2 and e1 plagioclases, the latter separates e1 and I1 plagioclases with only b reflections in their diffraction patterns from I1 and P1 samples having b and c reflections too. The first variation represents exactly the e2→e1 phase transitions, whereas the second one corresponds in good approximation to the C1→I1 transition, which has been determined at ~An70 by previous works. The I1→P1 phase transition in the anorthite-rich side of the solid solution is not highlighted in the collected Raman spectra. Variations in peak broadening provide insights into the behaviour of the order parameter on a local scale, suggesting an increase in the structural disorder within the solid solution, as the structures have to incorporate more Al atoms to balance the change from monovalent to divalent cations. All the information acquired on these natural plagioclases has been used to produce a protocol able to give a preliminary estimation of the chemical composition of an unknown plagioclase from its Raman spectrum. Two calibration curves, one for albite-rich plagioclases and the other one for the anorthite-rich plagioclases, have been proposed by relating the peak linewidth of the most intense Raman band υa and the An content. It has been pointed out that the dependence of the composition from the linewidth can be obtained only for low structural plagioclases with a degree of order not far away from the references. The proposed tool has been tested on three mineralogical samples, two of meteoric origin and one of volcanic origin. Chemical compositions by Raman spectroscopy compare well, within an error of about 10%, with those obtained by elemental techniques. Further analyses on plagioclases with unknown composition will be necessary to validate the suggested method and introduce it as routine tool for the determination of the chemical composition from Raman data in planetary missions.