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A halogen-substituted cyclic disilene compound, bromocyclotrisilene, Si 3 Br(Eind) 3 ( 3a ), bearing fused-ring bulky Eind ( a : R 1 = R 2 = Et) groups, has been synthesized as an extraordinarily air-stable compound by the reduction of 1,2-dibromodisilene, (Eind)BrSi═SiBr(Eind) ( 2a ), or tribromosilane, (Eind)SiBr 3 ( 1a ), with the Mg or Li metal. The X-ray diffraction analysis of 3a showed that the disilene moiety has an almost planar, but slightly trans -bent structure. Even though 3a is quite air-stable both in solutions and in the solid state, its Si-Br bond is reactive under reducing conditions. The further treatment of 3a with the Li metal leads to the formation of room-temperature thermally stable silicon homologues of the cyclopropyl radical, i.e., the cyclotrisilanyl radicals ( 6a ) [ 6a ( syn ) and 6a ( anti )], via intramolecular C-H bond activation in a transient silicon homologue of the cyclopropenyl radical, i.e., the cyclotrisilenyl radical, [Si 3 (Eind) 3 ] • ( 5a ). The formation mechanism of 6a from 5a is discussed based on the theoretical calculations. The unique structural and electronic properties of these Si 3 three-membered ring species incorporating the Eind groups have been experimentally and theoretically investigated.

Transition metal atom (M)-encapsulating silicon cage nanoclusters (M@Si 16 ) exhibit a superatomic nature, depending on the central M atom owing to the number of valence electrons and charge state on organic substrates. Since M@Si 16 superatom featuring group 4 and 5 transition metal atoms exhibit rare-gas-like and alkali-like characteristics, respectively, group 6 transition metal atoms are expected to show alkaline earth-like behavior. In this study, M@Si 16 , comprising a central atom from group 6 (M VI = Cr, Mo, and W) were deposited on C 60 substrates, and their electronic and chemical stabilities were investigated in terms of their charge state and chemical reactivity against oxygen exposures. In comparison to alkali-like Ta@Si 16 , the extent of charge transfer to the C 60 substrate is approximately doubled, while the oxidative reactivity is subdued for M VI @Si 16 on C 60 , especially for W@Si 16 . The results show that a divalent state of M VI @Si 16 2+ appears on the C 60 substrate, which is consistently calculated to be a symmetrical cage structure of W@Si 16 , revealing insights into the "periodic law" of M@Si 2+ in C 3 v , revealing insights into the "periodic law" of M@Si 16 superatoms pertaining to the characteristics of alkaline earth metals.

In organic reactions, bond-forming and bond-cleaving processes are generally considered to be more important than other processes such as conformational isomerization. We report herein an example where a conformational isomerization process, propeller-like alkene rotation, is considered to determine the selectivity over the reaction pathways. The transition state with the highest energy barrier in some alkylpalladium isomerization (chain walking) events was theoretically indicated to correspond to alkene rotation, while transition states for bond-cleaving β-hydride elimination and bond-forming migratory insertion were not even observed. It was also suggested both theoretically and experimentally that the palladium chain walking over internal carbons in alkyl chains proceeds via cis alkene intermediates rather than thermodynamically more stable trans alkene intermediates, due to their relative difficulty to undergo alkene rotation.

Elemental substitution and doping validate the optimization of chemical and physical properties of functional materials, and the composition ratio of the substituting atoms generally determines their properties by changing their geometric and electronic structures. For atomically precise nanoclusters (NCs) consisting of countable atom aggregates, the composition can be controlled accurately to provide an ideal model to study the heteroatom substitution effects. Since aluminum (Al) and boron (B) both belong to group 13 in the periodic table, the effect of B atom substitution on Al n NCs can be investigated while maintaining the total number of valence electrons in Al n B m NCs. In this study, oxidative reactivities of small Al NCs with B atom substitution are studied for Al n B m NCs ( m = 1, n = 6-14 and m = 2, n = 11) supported on organic surfaces by using X-ray photoelectron spectroscopy and oxygen molecule (O 2 ) exposure measurements. Before completing the endohedral B@Al 12 - superatomic NC, one B atom substitution in Al NCs (Al n B) enhances oxidative reactivities 3-20 times compared to those of Al n +1 , particularly for n ≤ 11. When one Al atom of Al 12 B is further substituted by a B atom to form Al 11 B 2 , the reactivity drastically increases (6.6 × 10 2 times), showing that the B atom substitution makes the NC chemically active or inactive geometrically depending on the exohedral or endohedral site for the B atom in the Al NC. In addition, density functional theory calculations show that the electronegative B atom contributes to forming a locally positive Al site to facilitate O 2 adsorption except in Al 12 B, in which the B atom is geometrically shielded by the surface of the Al 12 cage in B@Al 12 .

Cyclometalated iridium(III) complexes have been used in various optical materials, including organic light-emitting diodes (OLEDs) and photocatalysts, and a deeper understanding and prediction of their luminescence quantum yields (LQYs) greatly aid in accelerating material design. In this study, we integrated density functional theory (DFT) calculations with machine learning (ML) techniques to extract factors controlling LQY. Although a substantial data set of Ir(III) complexes and their LQYs is indispensable for constructing accurate ML models to predict LQYs, generating this type of data set is challenging due to the complexities associated with ab initio calculations of LQYs. To address this issue, we investigated the nonradiative decay process of nine Ir(III) complexes emitting blue to green, each exhibiting varying experimental LQYs, by using DFT calculations. For all nine complexes, the quenching process was induced by the rotation of the single bond in one of the ligands, which converted the six-coordinate structure to the five-coordinate structure. Since the decay mechanism was common for the nine Ir(III) complexes, parameters correlated with LQYs could be used as objective variables instead of LQYs. Based on this idea, we collected a data set featuring Ir(III) complexes and the energy differences between their six- and five-coordinate triplet structures, which correlated with LQYs. We also constructed ML models using the calculated LQYs as the objective variables with the parameters from the ground-state calculations as explanatory variables. The analyses of the constructed model revealed that the LUMO energy of the ligand made the most significant negative contribution to LQY. This suggests that the potential energy surface of the metal-to-ligand charge transfer (MLCT) excited state, which stabilizes the six-coordinate structure, is reduced by decreasing the energy of the unoccupied orbitals.

The structural and dynamical properties of water can be greatly altered by the anisotropic interfacial environment. Here, we study the intermolecular vibration and relaxation dynamics of a water film and a water droplet on a graphene surface based on low-frequency Raman spectra calculated from molecular dynamics simulations. The calculated Raman spectra of the interfacial water systems show a weakened libration peak and an enhanced intermolecular hydrogen bond (HB) stretching peak compared to the spectrum of bulk water, which are attributed to softened orientation motion. We also find that the collective polarizability relaxation in the droplet is much slower than that in the film and bulk, which is completely different from the collective dipole relaxation. The slow relaxation is due to a positive correlation between the induced polarizabilities of distinct molecules caused by the global and anisotropic structural fluctuations of the water droplet. Furthermore, we find that the two-dimensional HB network by the orientation-ordered interfacial water molecules leads to different intermolecular vibration dynamics between the parallel and perpendicular components. The present theoretical study demonstrates that low-frequency Raman spectroscopy can reveal the anisotropic and finite effects on the intermolecular dynamics of the water film and droplet.

Fourier-transform infrared (FTIR) spectroscopy can detect the presence of functional groups and molecules directly from a mixed solution of organic molecules. Although it is quite useful to monitor chemical reactions, quantitative analysis of FTIR spectra becomes difficult when various peaks of different widths overlap. To overcome this difficulty, we propose a chemometrics approach to accurately predict the concentration of components in chemical reactions, yet interpretable by humans. The proposed method first decomposes a spectrum into peaks with various widths by the wavelet transform. Subsequently, a sparse linear regression model is built using the wavelet coefficients. Models by the method are interpretable using the regression coefficients shown on Gaussian distributions with various widths. The interpretation is expected to reveal the relation of broad regions in spectra to the model prediction. In this study, we conducted the prediction of monomer concentration in copolymerization reactions of five monomers against methyl methacrylate by various chemometric approaches including conventional methods. A rigorous validation scheme revealed that the proposed method overall showed better predictive ability than various linear and non-linear regression methods. The visualization results were consistent with the interpretation obtained by another chemometric approach and qualitative evaluation. The proposed method is found to be useful for calculating the concentrations of monomers in copolymerization reactions and for the interpretation of spectra., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

By means of an initial electrochemical carbon dioxide reduction reaction (eCO 2 RR), both the reaction current and Faradaic efficiency of the eCO 2 RR on boron-doped diamond (BDD) electrodes were significantly improved. Here, this effect is referred to as the self-activation of BDD. Generally, the generation of carbon dioxide radical anions (CO 2 •- ) is the most recognized pathway leading to the formation of hydrocarbons and oxygenated products. However, the self-activation process enabled the eCO 2 RR to take place at a low potential, that is, a low energy, where CO 2 •- is hardly produced. In this work, we found that unidentate carbonate and carboxylic groups were identified as intermediates during self-activation. Increasing the amount of these intermediates via the self-activation process enhances the performance of eCO 2 RR. We further evaluated this effect in long-term experiments using a CO 2 electrolyzer for formic acid production and found that the electrical-to-chemical energy conversion efficiency reached 50.2% after the BDD self-activation process., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Catalytic asymmetric Mannich reactions of imines with weakly acidic simple amides were developed using a chiral potassium hexamethyldisilazide (KHMDS)-bis(oxazoline) potassium salt (K-Box) catalyst system. The desired reactions proceeded to afford the target compounds in high yields with high diastereo- and enantioselectivities. It was suggested that a K enolate interacted with K-Box to form a chiral K enolate that reacted with imines efficiently. In this system, K-Box (potassium salt of Box) worked as a chiral ligand of the active potassium species.

Monodisperse ceria-zirconia nanoparticles have attracted much attention as potential high-performance catalysts. Acidic aqueous solutions are generally used for peptizing aggregated precipitates during the fabrication of disperse nanoparticles. However, the peptization process requires multiple hours of aging, which significantly decreases the production efficiency. Hence, various researchers have attempted to eliminate this stage altogether by performing a coprecipitation process under ambient conditions using common salts as the starting materials. In this work, we report a continuous and direct technique for the fabrication of monodisperse composite oxide nanoparticles via coprecipitation inside a novel high-shear agitation reactor without aging. Using this method, monodisperse ceria-zirconia-yttria composite oxide nanoparticles with diameters of 3 nm were successfully synthesized., Competing Interests: The authors declare no competing financial interest.

The structural preference of [7]circulene is analyzed by taking into account vibronic interactions. DFT calculations reveal that pseudo-Jahn-Teller effects cause the D7h-symmetry structure to relax to C2- and Cs-symmetry structures, which are both ca. 9 kcal/mol lower in energy than the D7h structure. In energy terms, the C2-symmetry structure is 0.05 kcal/mol lower than that of the Cs-symmetry. The active vibrations are attributed to low-frequency puckering modes that are coupled with π-σ excitation states. The optical activities of the C2-symmetry structure were simulated by configuration interaction calculations, and the simulated CD/ORD spectra were reasonable and consistent with the experimental data. The optical rotatory strengths obeyed the helix rule; that is, the left-handed helix shows negative Cotton effects through the antisymmetric excited states. The calculated spectra will serve as a foundation for further investigation of optical activities of negatively curved structures.

Density functional theory (DFT), combined with the artificial force-induced reaction (AFIR) method, is used to establish the mechanism of the aqueous Mukaiyama aldol reactions catalyzed by a chiral Fe(II) complex. On the bases of the calculations, we identified several thermodynamically stable six- or seven-coordinate complexes in the solution, where the high-spin quintet state is the ground state. Among them, the active intermediates for the selectivity-determining outer-sphere carbon-carbon bond formation are proposed. The multicomponent artificial force-induced reaction (MC-AFIR) method found key transition states for the carbon-carbon bond formation, and explained the enantioselectivity and diastereoselectivity. The overall mechanism consists of the coordination of the aldehyde, carbon-carbon bond formation, the rate-determining proton transfer from water to aldehyde, and dissociation of trimethylsilyl group. The calculated full catalytic cycle is consistent with the experiments. This study provides important mechanistic insights for the transition metal catalyzed Mukaiyama aldol reaction in aqueous media.

The recently developed artificial force induced reaction (AFIR) method was applied to search systematically all possible multicomponent pathways for the Biginelli reaction mechanism. The most favorable pathway starts with the condensation of the urea and benzaldehyde, followed by the addition of ethyl acetoacetate. Remarkably, a second urea molecule catalyzes nearly every step of the reaction. Thus, the Biginelli reaction is a urea-catalyzed multicomponent reaction. The reaction mechanism was found to be identical in both protic and aprotic solvents.

Planktonic metabolism plays crucial roles in Earth's elemental cycles. Chemical speciation as well as elemental stoichiometry is important for advancing our understanding of planktonic roles in biogeochemical cycles. In this study, a multicomponent solid-state nuclear magnetic resonance (NMR) approach is proposed for chemical speciation of cellular components, using several advanced NMR techniques. Measurements by ssNMR were performed on (13)C and (15)N-labeled Euglena gracilis, a flagellated protist. 3D dipolar-assisted rotational resonance, double-cross-polarization (1)H-(13)C correlation spectroscopy, and (1)H-(13)C solid-state heteronuclear single quantum correlation spectroscopy successively allowed characterization of cellular components. These techniques were then applied to E. gracilis cultured in high and low ammonium media to demonstrate the power of this method for profiling and comparing cellular components. Cellular NMR spectra indicated that ammonium induced both paramylon degradation and amination. Arginine was stored as a nitrogen reserve and ammonium replaced by arginine catabolism via the arginine dihydrolase pathway. (15)N and (31)P cellular ssNMR indicated arginine and polyphosphate accumulation in E. gracilis, respectively. This chemical speciation technique will contribute to environmental research by providing detailed information on environmental chemical properties.

Protomeric tautomerism is analyzed in view of the topological charge stabilization rules. Based on Hückel molecular orbital considerations and modern DFT calculations, it was found that the branching of amino or hydroxyl groups significantly contributes to the stability of major species through the first- and second-order perturbations with respect to the isoelectronic hydrocarbon. While amino-imino tautomerism is almost completely dominated by topological charge stabilization, hydroxyl-oxo tautomerism is affected by changes in the resonance integral of C-O/C═O bonds. Nevertheless, apart from side effects such as hydrogen bonds or solvent effects, a quantitative preference rule for the prediction of the tautomeric stability can be developed using topological π-electron energetics. As well as the analyses of simple bases, applications to complex or extended systems are exemplified analyzing purine bases, polyguanide, and polyuret. The present approach can be useful in conjunction with chemical intuition that comes from conventional valence bond theory.

Lanthanide complexes with temperature dependent f-f emission intensities are commonly used as temperature sensors. The thermosensitivity can be controlled by the ligands, but their effects are difficult to predict. To clarify the origin of the differences in thermosensitivity, we propose a new theoretical strategy, the energy shift method, and use it to find crossing points between two states where intersystem crossing and excitation energy transfer take place. The different sensitivities of the three studied terbium(III) complexes are caused by the different rate-determining steps for emission or quenching.

C6I6(2+) has been reported to have a σ-aromatic character since removal of two σ anti-bonding electrons localized on iodines results in fulfilling Hückel (4n+2) rules for I6(2+) as well as C6 parts. To search for molecules possessing similar character, hexa-group 16 atom-substituted benzene dications C6(ChH)6(2+) (Ch = S, Se, Te) and their derivatives are examined for aromatic character by using nucleus-independent chemical shift (NICS). For these dications, in which iodines in C6I6(2+) are replaced by group 16 atoms, negative NICS values larger in magnitude than for benzene are found when a σ anti-bonding orbital localized on group 16 atoms is unoccupied. To clarify the origin of large negative NICS values, they are decomposed into individual molecular orbitals. It has been shown that both π bonding orbitals on C6 and σ bonding orbitals on Se6 or Te6 contribute to the negative NICS values, indicating that the aromaticity of these dications have a substantial σ character as well as π characters. Aromaticity of group 14 and 15 atom-substituted benzene dications is also discussed.

Carbon-carbon bond formations, such as Kobayashi modification of the Mukaiyama-Aldol reaction, catalyzed by lanthanide (Ln) Lewis acid in aqueous solution comprise one of the most attractive types of reactions in terms of green chemistry. However, their detailed mechanisms and the role of water molecules remained unclear. In order to explore complex potential energy surfaces for the water and substrate coordination around Eu(3+) as well as the detailed mechanism of the Mukaiyama-Aldol reaction between trimethylsilyl (TMS) cylcohexenolate and benzaldehyde (BA) catalyzed by Eu(3+), the recently developed anharmonic downward distortion following (ADDF) and artificial force-induced reaction (AFIR) methods were used with the B3LYP-D3 theory. The most favorable water coordination structures are Eu(3+)(H2O)8 and Eu(3+)(H2O)9; they are comparable in free energy and are likely to coexist, with an effective coordination number of 8.3. Eu(3+)(H2O)8(BA) is the best aldehyde coordinated structure. Starting with this complex, the Mukaiyama-Aldol reaction proceeds via a stepwise mechanism, first C-C bond formation between the substrates, followed by proton transfer from water to BA and then TMS dissociation caused by nucleophilic attack by bulk water molecules. Why did the yield of the Mukaiyama-Aldol reaction catalyzed by Ln(3+) in organic solvent dramatically increase upon addition of water? Without water, the reverse reaction (C-C cleavage) takes place easily. Why did this reaction show syn-preference in water? The anti transition state for C-C formation in water is entropically less favored relative to the syn transition state because of the existence of a rigid hydrogen bond between the TMS part and coordination water around Eu(3+) in the former.

To predict the stereoselectivity of large and flexible reaction systems, structural sampling of many transition states (TSs) is required. We used an automated search method, the artificial force induced reaction (AFIR) method, for TS sampling and found 91 syn- and 73 anti-TSs for the diastereoselective C-C bond formation step of the aqueous lanthanide-catalyzed Mukaiyama aldol reaction. Among them 11 syn- and six anti-TSs are found to contribute significantly to the diastereomeric ratio at room temperature.

A new method for the synthesis of macrocyclic lactones, lactams, and ketones, which utilizes photoinduced intramolecular radical cyclization reactions of substrates containing tethered carboxylic acids and α,β-unsaturated carbonyl moieties, has been uncovered. Photocyclization of the carboxylic acids tethered acrylate ester, which were prepared starting from the macrocyclic lactones, gave the two-carbon elongated macrocyclic lactones via decarboxylation. Similar photoreactions of carboxylic acid tethered acryl amide or α,β-unsaturated ketone moieties, which were also prepared starting from the macrocyclic lactones, produced macrocyclic lactams or ketones, respectively. The simple approach can be readily applied to the preparation of a variety of macrocyclic lactones, lactams, and ketones with tunable ring sizes.

Development of efficient methods for finding chemical reaction pathways has been one of the central subjects of theoretical chemistry. Recently, the artificial force induced reaction (AFIR) method enabled automated search for associative reaction pathways between multiple reactant molecules and has been applied to reactions involving a few tens of atoms. To expand its applicability to large systems, we combined it with the geometrical microiteration technique. With this extension, full optimization of transition state structures of enzymatic reactions in the protein became possible within the QM/MM framework. Performance of the microiteration-AFIR method was tested for a single water catalyzed Aldol reaction in (H2O)299 cluster and for an enzymatic reaction of the isopenicillin N synthase, where the potential energy surfaces were calculated by the ONIOM(QM/MM) method. These numerical tests demonstrated that the present method is promising in predicting reaction pathways that take place within an active site (consisting of tens of atoms) in a very large environment such as protein and solution.

An enantioselective synthesis of tetrahydropyrrolo[1,2-c]pyrimidine-1,3-diones via a palladium-catalyzed intramolecular oxidative aminocarbonylation is described. The carbon-carbon double bond of alkenylurea substrates has been shown to react intramolecularly with a nitrogen nucleophile in the presence of a palladium catalyst under a carbon monoxide atmosphere. The use of a chiral spiro bis(isoxazoline) ligand (SPRIX) is essential to obtain the desired products in optically active forms. In comparison with the coordination ability of other known ligands, this peculiar character of SPRIX originates from two structural characteristics: low sigma-donor ability of the isoxazoline coordination site and rigidity of the spiro skeleton.

The photoabsorption intensities of intra-4f(N) transitions (f-f transitions) in lanthanide systems have been extensively studied with the semiempirical Judd-Ofelt theory. The oscillator strengths of most f-f transitions are insensitive to a change of surrounding environment because 4f electrons are shielded by closed-shell 5s and 5p electrons from outside. However, there are some exceptional transitions, so-called hypersensitive transitions, whose intensities are very sensitive to a change of surrounding environment, and the reason for this hypersensitivity has not been clarified. In this study, we calculated the oscillator strengths of lanthanide trihalides (LnX(3); Ln = Pr, Tm; X = Br, I) with the multireference spin-orbit configuration interaction method and obtained reasonably accurate values. To clarify the cause of hypersensitivity, we examined various possible effects on the oscillator strengths, such as molecular vibration, f-d mixing, ligand to metal charge transfer (LMCT), and intraligand excitation, and concluded that the effect of molecular vibration is very small and that the oscillator strengths of most f-f transitions including hypersensitive transitions arise from both the LMCT and dynamic-coupled intraligand excitations through their configuration mixings with the dominant configurations of 4f(N).

Inter- and intramolecular additions of alkyl radicals, generated by SET photochemical decarboxylation reactions of free carboxylic acids, to electron-deficient alkenes take place under mild conditions as part of efficient routes for the formation of N-Boc gamma-amino acids and macrocyclic lactones.

The first asymmetric Pd(II)/Pd(IV) catalysis has been achieved by employing the combination of a hypervalent iodine reagent and a chiral ligand, SPRIX. Enantioselective cyclization of enyne derivatives catalyzed by the Pd-i-Pr-SPRIX complex furnished lactones bearing a bicyclo[3.1.0]hexane skeleton with up to 95% ee.

The bulky and amphiphilic nature of tryptophan residues makes them particularly interesting components of proteins. In bacteriorhodopsin, four of the eight tryptophan residues are in the active site, forming parts of the retinal binding pocket. In this work, we use solid-state NMR to study the interactions of the tryptophan residues in wild-type bacteriorhodopsin, in the resting state, and in critical intermediates of the proton-motive photocycle. The range of the chemical shifts of the indole nitrogens suggests that all eight of them are hydrogen bonded. Using difference spectroscopy, we isolate several changes in these hydrogen bonds in the early and late M states. As found earlier for the peptide backbone, some perturbations found in the early M state relax in the transition to the late M state while new perturbations arise. Interestingly, Rotational Echo DOuble Resonance (REDOR) difference spectroscopy of [20-13C]retinal,[indole-15N]Trp-bR shows that indole of Trp182 is not involved in the significant hydrogen bond perturbations. We also use REDOR to measure dipolar interactions in [20-13C]retinal,[indole-15N]Trp-bR, and thereby determine the distance between the C20 of retinal and the indole nitrogen of Trp182. The internuclear distance changes only slightly from the light-adapted state (3.36 +/- 0.2 A) to the early M state (3.16 +/- 0.4 A).

Illumination of the Trp86 --> Phe mutant of bacteriorhodopsin causes anomalous light adaptation, i.e., isomerization of the retinal from all-trans to 13-cis, 15-syn. FTIR spectral analysis shows that illumination at 250 K yields two 13-cis photoproducts, the conventional 13-cis, 15-syn state, BR(C), and another termed BR(X). BR(X) is different from BR(C) because it has a lower N-H in-plane bending frequency and a higher C14-C15 stretching frequency, as well as an absence of coupling between these modes. BR(X), which is stable at 275 K, is more abundant in the photosteady state produced by longer wavelength light and detected as the only photoproduct at 170 K. Its different structural features result from distortion of the C14-C15 bond of the chromophore. In the W86F mutant protein, the small structural changes of a water molecule in the conversion between the all-trans and 13-cis, 15-syn forms and in the formation of the K photointermediate are absent, but the larger changes of water molecule(s) that normally occur in the L and M intermediates are present. We propose that Trp86, together with Asp85, is involved in binding the water molecule and in preventing the formation of the 13-cis, 15-syn photoproducts, BR(C) and BR(X), when the wild type protein is illuminated.

The last intermediate in the photocycle of the light-driven proton pump bacteriorhodopsin is the red-shifted O state. The structure and dynamics of the last step in the photocycle were characterized with time-resolved Fourier transform infrared spectroscopy of the mutants of Glu-204 and Leu-93, which accumulate this intermediate in much larger amounts than the wild type. The results show that E204Q and E204D give distorted all-trans-retinal chromophore like the O intermediate of the wild type. This is simply due to the perturbation of the proton acceptor function of Glu-204 in the O-to-BR transition in the Glu-204 mutants. The corresponding red-shifted intermediates of L93M, L93T, and L93S have a 13-cis chromophore like the N intermediate of the wild type, as reported from analysis of extracted retinal [Delaney, J. K., Schweiger, U., & Subramaniam, S. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 11120-11124]. In spite of their different chromophore structures from the O intermediate, the red-shifted intermediates are similar to the O intermediate but not to the N intermediate of the wild type with respect to structural changes in the peptide carbonyls. The structural changes around Asp-96 in the N intermediate are completely restored also in the red-shifted intermediates of the Leu-93 mutants like in the O intermediate. These results imply that the protein structural changes in the last step proceed regardless of thermal isomerization of the chromophore. Time-resolved Fourier transform infrared spectroscopy with the Glu-204 mutants suggests that the response of Asp-204 (Glu-204 in the wild type) to the protonation of Asp-85 during formation of the M intermediate, which results in proton release, is slow and may occur through structural changes.

Arg82, one of the residues near the protonated Schiff base of bacteriorhodopsin, facilitates proton release to the medium during the L-to-M reaction of the photocycle, but retards the rate of proton transfer from the Schiff base to Asp85. In order to understand the role of Arg82 in these processes, the structural changes upon formation of the M intermediate were studied by Fourier transform infrared spectroscopy of the hydrated films of Arg82 mutants at pH 9.5. The negative band at 1700 cm-1 in the BR --> M spectrum due to the deprotonation of Glu204 was absent when Arg82 was replaced with alanine (R82A), but present with small amplitude when residue 82 was a glutamine (R82Q), or a lysine (R82K), with a shift to 1696 cm-1. The O-H stretch of water at 3643 cm-1 is shifted toward a lower frequency in R82Q, R82K, and R82A in the unphotolyzed state. However, R82Q retains a fraction of the unshifted band. Another O-H stretch is prominent in R82Q around 3625 cm-1 but absent in R82A and probably in R82K. In parallel, R82Q retains a fraction of the slow component of the formation of the M intermediate, which is almost completely absent in R82K and R82A. These results, along with previous data for the mutants of Glu204, suggest that the guanidium group of Arg82 influences the H-bonding of water molecules located close to Asp85 and Arg82-Glu204 regions, and the rate of proton transfer from the Schiff base to Asp85. The amide group of Gln82 can substitute for it but weakly.

During the L-->M reaction of the bacteriorhodopsin photocycle the proton of the retinal Schiff base is transferred to the anionic D85. This step, together with the subsequent reprotonation of the Schiff base from D96 in the M-->N reaction, results in the translocation of a proton across the membrane. The first of these critical proton transfers occurs in an extended hydrogen-bonded complex containing two negatively charged residues (D85 and D212), two positively charged groups (the Schiff base and R82), and coordinated water. We simplified this region by replacing D212 and R82 with neutral residues, leaving only the proton donor and acceptor as charged groups. The D212N/R82Q mutant shows essentially normal proton transport, but in the photocycle neither of this protein nor of the D212N/R82Q/D96N triple mutant does a deprotonated Schiff base (the M intermediate) accumulate. Instead, the photocycle contains only the K, L, and N intermediates. Infrared difference spectra of D212N/R82Q and D212N/R82Q/D96N demonstrate that although D96 becomes deprotonated in N, D85 remains unprotonated. On the other hand, M is produced at pH > 8, where according to independent evidence the L<==>M equilibrium should shift toward M. Likewise, M is restored in the photocycle when the retinal is replaced with the 14-fluoro analogue that lowers the pKa of the protonated Schiff base, and now D85 becomes protonated as in the wild type.(ABSTRACT TRUNCATED AT 250 WORDS)

Fourier transform infrared spectra of the L intermediate of light-adapted bacteriorhodopsin were examined for recombinant proteins with amino acid substitutions at Thr46 and Asp96. Two O-H stretching vibrational bands of water, at 3607 and 3577 cm-1, change into stronger H-bonding states in L of the wild type. Thr46-->Val substitution abolished these bands in spite of the fact that [3-18O]threonine-labeling did not shift them, indicating that they correspond to coordination of the water with Thr46. The two water bands were restored, although with changed frequencies, by an additional Asp96-->Asn substitution in Thr46-->Val/Asp96-->Asn. A single Asp96-->Asn substitution abolished the 3607 cm-1 band. Thus, Asp96 also takes part in structural changes in water. The perturbations of these water molecules in the L intermediate displayed a weak correlation with the ratio of intensity change in the two vibrational bands of the Schiff base mode at 1312 and 1301 cm-1 and the rate for the deprotonation of the Schiff base at the L-to-M reaction of the photocycle. We find, therefore, that the water molecules in the cytoplasmic Asp96-Thr46 domain, which comprises the site of proton uptake after formation of the M intermediate, undergo structural changes in the L intermediate already. These changes are transmitted to the extracellular domain and affect interaction of the Schiff base with Asp85, that is far removed from this region.

An intense indole N-H stretching vibrational band at 3486 cm-1 in the difference Fourier transform infrared spectrum is one of the characteristic features of the L intermediate of bacteriorhodopsin [Maeda, Sasaki, Ohkita, Simpson, & Herzfeld (1992) Biochemistry 31, 12543]. This band is now assigned to tryptophan-182. The Trp182-->Phe (W182F) protein shows specific features in the difference spectrum in the visible region upon L formation, and exhibits great delay in the L-M conversion. Fourier transform infrared difference spectra further indicate that while the intensity of the C-methyl in-plane bending vibration at 1009 cm-1 is lost in the L intermediate of the wild type, its intensity remains high in the W182F protein. The intensity of the N-H stretching vibration upon L formation is diminished considerably in an artificial bacteriorhodopsin containing 9-desmethylretinal. It also exhibits delayed M formation. These results suggest that Trp182 interacts with the retinal side chain through the 9-methyl group, and thereby affects the L-to-M conversion.

Low and high Ca2+-requiring forms of Ca2+-dependent cysteine proteinase are known as calpain I and calpain II, respectively. We have obtained, for the first time, monospecific antibodies for calpain I and for calpain II. Using these antibodies and an electrophoretic blotting method, we have found that a small, but reproducible, amount of calpain I was associated with human erythrocyte membranes while the bulk of the protease was contained in the cytosol. Most of membrane-associated calpain I was extractable with 1% Triton X-100, but not with 0.1% detergent. In the presence of 0.1 mM Ca2+ and 5 mM cysteine, membrane-associated calpain I degraded the membrane protein band 4.1 preferentially and band 3 protein only slowly. The Ca2+-induced autodigestion of the membrane preparation was inhibited by leupeptin but not by a cytosolic calpain inhibitor, calpastatin, added to the incubation medium. No calpain II was detected in either erythrocyte cytosol or membranes when anti-calpain II antibody was used under the same conditions as those for the detection of calpain I.

Isolation and nucleotide sequencing of the complementary DNA for pig heart calpastatin have been completed. The amino acid sequence of 713 residues predicted from the nucleotide sequence contains five domains, each composed of approximately 140 amino acid residues. A unique N-terminal domain is followed by four mutually homologous domains. The best fit alignment of these four domains gives residue identities between any two domains of 22.5-36.0%. The analysis of the sequence similarities by several methods also suggests the existence of additional shorter repeats at intervals of 60-80 residues. The calculated molecular weight of pig calpastatin of 713 amino acid residues (Mr 77,122) is significantly lower than the value of purified pig heart calpastatin (Mr 107,000) estimated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS-PAGE). The expression of the calpastatin genes in Escherichia coli and the detection of the translation products of 713, 366, and 140 amino acid residues by the specific anti-calpastatin antibody indicate that the products always migrate considerably slow on SDS-PAGE, giving an average of 1.53 for the ratio of the molecular weight estimated by SDS-PAGE to the value calculated from the amino acid sequences. It is most likely that the discrepancy in the molecular weight is caused by an anomalous behavior of calpastatin in SDS-PAGE.