Magnesium spin state determines the energetics of an adenosinetriphosphate molecule

The molecular dynamics method (density functional theory) DFT:B3LYP (6-3IG** basis set, t = 310 K) was used to study interactions between a molecule of adenosinetriphosphate (ATP) (ATP subsystem) and the [Mg(H₂O)₆]²⁺ magnesium cofactor (Mg subsystem) in an aqueous medium simulated by 78 water molecules in the singlet (S) and triplet (T) states. Potential energy surfaces (PESs) for the S (lowest in energy) and T states (highest in energy) are significantly separated in space. Motion along them directs the Mg complex either to oxygen atoms of the γ-β-phosphate groups (O1–O2) (S state of PES) or to oxygen atoms of the β-α-phosphate groups (O2–O3) (T state of PES). Chelation of the γ-β- and β-α-phosphates leads to formation of a stable low-energy ([Mg(H₂O)₄-(OI-O2)ATP]^2?) complex or a metastable high-energy ([Mg(H₂O)₂-(O2–O3)ATP]^2?) complex, respectively, which differ in number of water molecules surrounding the Mg atom. Intersection of two T PESs is accompanied by formation of an unstable state characterized by redistribution of spins between the Mg and ATP subsystems. This state, being sensitive to interaction with the Mg nuclear spin (²⁵Mg), induces an unpaired electron spin, which initiates the ATP cleavage by the ion-radical mechanism, yielding a reactive ion radical of adenosinemonophosphate (·AMP^?), which was earlier found experimentally by the method of chemically induced dynamic nuclear polarization (CIDNP). Biological aspects of the results obtained are discussed.     

A first-principles study of Ni<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Pd<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (n = 1 − 5) clusters

A first-principle investigation of structures and properties of Ni _n Pd _n (n=1-5) clusters is presented. For this study, the linear combination of Gaussian-type orbitals auxiliary density functional theory (LCGTO-ADFT) method has been employed. In order to determine the lowest energy structures, several isomers in different spin multiplicities were studied, for each cluster size. Initial structures, for which successive geometry optimization was computed without any constrain, were taken along Born–Oppenheimer molecular dynamics (BOMD) trajectories. To discriminate between minima and transition state structures, harmonic frequency analyses were performed at the optimized structures. Ground state structures, bond lengths, harmonic frequencies, dissociation energy, ionization potential, electron affinity and spin density plots are presented. This work demonstrates, that the Pd atoms prefer to allocate on the surface of the cluster structures whose core is formed by the 3d TM atoms type. Moreover, it has been observed that the ground-state structure spin multiplicity increases as the system size grows. The results of this study contribute to gain insight into how structures and energy properties change with cluster size in bimetallic Pd-based alloys.     

Small Anion with Higher Valency Retards the Compaction of DNA in the Presence of Multivalent Cation

It has been established that, upon the addition of multivalent cations, long DNA chains in an aqueous solution exhibit a remarkable discrete transition from a coil state to a compact state at the level of a single chain. In this study, we investigated the polyelectrolyte nature of DNA with the experimental methodology of single-DNA observation, and provide a theoretical interpretation. We examined the effects of co-ions with different valencies (Cl⁻, SO₄²⁻, PO₄³⁻) on DNA compaction. As a result, we found that co-ions with a greater valency induce the coil state rather than the compact state. Based on a simple model with mean-field approximation that considered ion pairing, we show how the increase in entropy of small ions contributes to the stability of the compact state, by overcoming entropic penalties such as elastic confinement of the chain and a decrease in the translational freedom of counterions accompanied by charge neutralization.     

Segmental flexibility of ribosomal protein S1 bound to ribosomes and Q beta-replicase

The protonization pattern of the endogenous donor component D₁ which feeds electrons directly into chl-a⁺_II has been analyzed in Tris-washed inside-out thylakoids with the aid of appropriate pH-indicators. It was found that under repetitive flash excitation the amount of protons released is proportional to the extent of D₁-oxidation, depending on the time between the flashes. The kinetics of D₁-oxidation (being practically the same as in normal Tris-washed chloroplasts) are faster than the proton release by two orders of magnitude. The results lead to the conclusion that D₁ is protonized in the reduced state with pK(D^ox₁) < 5 and becomes deprotonized in the oxidized state with pK(D^red₁) ? 8. The proton release is kinetically limited by a transport barrier. Implications on the interpretation of the proton release pattern in preparation with intact water oxidation are discussed.     

Chemically induced lipid phase separation in model membranes containing charged lipids: A spin label study

The lipid distribution in binary mixed membranes containing charged and uncharged lipids and the effect of Ca²⁺ and polylysine on the lipid organization was studied by the spin label technique. Dipalmitoyl phosphatidic acid was the charged, and spin labelled dipalmitoyl lecithin was the uncharged (zwitterionic) component. The ESR spectra were analyzed in terms of the spin exchange frequency, W_ex. By measuring W_ex as a function of the molar percentage of labelled lecithin a distinction between a random and a heterogeneous lipid distribution could be made. It is established that mixed lecithinphosphatidic acid membranes exhibit lipid segregation (or a miscibility gap) in the fluid state. Comparative experiments with bilayer and monolayer membranes strongly suggest a lateral lipid segregation. At low lecithin concentration, aggregates containing between 25% and 40% lecithin are formed in the fluid phosphatidic acid membrane. This phase separation in membranes containing charged lipids is understandable on the basis of the Gouy-Chapman theory of electric double layers.In dipalmitoyl lecithin and in dimyristoyl phosphatidylethanolamine membranes the labelled lecithin is randomly distributed above the phase transition and has a coefficient of lateral diffusion of D = 2.8·10^?8 cm²/s at 59°C.Addition of Ca²⁺ dramatically increases the extent of phase separation in lecithin-phosphatidic acid membranes. This chemically (and isothermally) induced phase separation is caused by the formation of crystalline patches of the Ca²⁺-bound phosphatidic acid. Lecithin is squeezed out from these patches of rigid lipid. The observed dependence of W_ex on the Ca²⁺ concentration could be interpreted quantitatively on the basis of a two-cluster model. At low lecithin and Ca²⁺ concentration clusters containing about 30 mol% lecithin are formed. At high lecithin or Ca²⁺ concentrations a second type of precipitation containing 100% lecithin starts to form in addition. A one-to-one binding of divalent ions and phosphatidic acid at pH 9 was assumed. Such a one-to-one binding at pH 9 was established for the case of Mn²⁺ using ESR spectroscopy.Polylysine leads to the same strong increase in the lecithin segregation as Ca²⁺. The transition of the phosphatidic acid bound by the polypeptide is shifted from T_t = 47.5° to T_t = 62°C. This finding suggests the possibility of cooperative conformational changes in the lipid matrix and in the surface proteins in biological membranes.     

Photoluminescence of Dy3+ activator sensitized by Ce3+ in KNaSO4 microphosphor

The KNaSO₄ microphosphor doped with Ce or Ce and Dy prepared by a wet chemical method was studied by scanning electron microscopy (SEM) and characterized by photoluminescence (PL). KNaSO₄ has a 5‐µm particle size detected by SEM. The KNaSO₄:Ce³⁺ spectrum shows a single emission band at 327 nm for an excitation of 269 nm due to 5d → 4f transition of the Ce³⁺ ion, indicating weak spin orbiting coupling of the Ce³⁺ ground state. Efficient energy transfer takes place from Ce³⁺ → Dy³⁺ sublattices indicating that Ce³⁺ could effectively sensitize Dy³⁺ (orange emission) and that the Ce³⁺ emission weakens significantly in KNaSO₄. The powder form of prepared KNaSO₄ show negligible change in morphologies and hence no effect on the particle size. The characteristics of this powder could provide improved luminescence properties. The development and understanding of this photoluminescence and the effect of Dy³⁺ on KNaSO₄: Ce³⁺ are discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

Conformational effect of a spin crossover iron(II) complex: Bis[N-(2-methylimidazol-4-yl)methylidene-2-aminoethyl]propanediamineiron(II) perchlorate

A iron(II) complex of the linear hexadentate N₆ ligand H₂L^2-3-2, [Fe(H₂L^2-3-2)](ClO₄)₂, was synthesized and the spin crossover properties were investigated, where H₂L^2-3-2 denotes bis[N-(2-methylimidazol-4-yl)methylidene-2-aminoethyl]propanediamine. The complex showed a gradual and reversible one-step spin crossover (SCO) between the high-spin (S = 2) and low-spin (S = 0) states at T_1/2 = 208 K without hysteresis. The crystal structures were determined at 296 and 250 K (HS state), 230, 210, and 200 K (intermediate between the HS and LS states) and 150 and 110 K (LS state). The spin transition from 296 to 150 K accompanies with the conformation change of the chelate rings at the triamine moiety and the formation of the hydrogen bond network in the same space group of orthorhombic Pbcn (no. 60). However, in the LS state at 110 K, the space group changed from orthorhombic Pbcn at 150 K (Pcan when the same axial setting to 110 K was used) to monoclinic P2₁/a (no. 14) at 110 K, although no spin transition and no change of assembly structure between 150 and 110 K were observed. It give us an idea that the space group transformation is mainly related to the conformational thermodynamic stability of the chelate rings at the triamine moiety and is not directly correlated with the spin transition.     

Differential Control of Xanthophylls and Light-Induced Stress Proteins, as Opposed to Light-Harvesting Chlorophyll a/b Proteins, during Photosynthetic Acclimation of Barley Leaves to Light Irradiance

Barley (Hordeum vulgare L.) plants were grown at different photon flux densities ranging from 100 to 1800 μmol m⁻² s⁻¹ in air and/or in atmospheres with reduced levels of O₂ and CO₂. Low O₂ and CO₂ partial pressures allowed plants to grow under high photosystem II (PSII) excitation pressure, estimated in vivo by chlorophyll fluorescence measurements, at moderate photon flux densities. The xanthophyll-cycle pigments, the early light-inducible proteins, and their mRNA accumulated with increasing PSII excitation pressure irrespective of the way high excitation pressure was obtained (high-light irradiance or decreased CO₂ and O₂ availability). These findings indicate that the reduction state of electron transport chain components could be involved in light sensing for the regulation of nuclear-encoded chloroplast gene expression. In contrast, no correlation was found between the reduction state of PSII and various indicators of the PSII light-harvesting system, such as the chlorophyll a-to-b ratio, the abundance of the major pigment-protein complex of PSII (LHCII), the mRNA level of LHCII, the light-saturation curve of O₂ evolution, and the induced chlorophyll-fluorescence rise. We conclude that the chlorophyll antenna size of PSII is not governed by the redox state of PSII in higher plants and, consequently, regulation of early light-inducible protein synthesis is different from that of LHCII.     

On the nature of the g = 6 EPR signal in isolated cytochrome b6f complex from spinach chloroplasts

Cytochrome b₆ in freshly prepared, active cytochrome t₆f complex from spinach chloroplasts shows a broad, low-spin EPR signal around g_z = 3.6. Maximally half of the hemes of cytochrome b₆ can be changed to high spin with a signal at g = 6 by inactivating treatments, or by isolating cytochrome b₆. In this state the heme reacts with NO. Reduction rates suggest that it is the low-potential heme which changes. The change is accompanied by the loss of the shift in the g_y signal of the Rieske FeS-center by quinone analogs.     

Towards a spin coupling model for the Mn4 cluster in Photosystem II

The X-band EPR spectra of the IR sensitive untreated PSII and of MeOH- and NH₃-treated PSII from spinach in the S₂-state are simulated with collinear and rhombic g- and Mn-hyperfine tensors. The obtained principal values indicate a 1Mn(III)3Mn(IV) composition for the Mn₄ cluster. The four isotropic components of the Mn-hyperfine tensors are found in good agreement with the previously published values determined from EPR and ⁵⁵Mn-ENDOR data. Assuming intrinsic isotropic components of the Mn-hyperfine interactions identical to those of the Mn-catalase, spin density values are calculated. A Y-shape 4J-coupling scheme is explored to reproduce the spin densities for the untreated PSII. All the required criteria such as a S=1/2 ground state with a low lying excited spin state (30 cm⁻¹) and an easy conversion to a S=5/2 system responsible for the g=4.1 EPR signal are shown to be satisfied with four antiferromagnetic interactions lying between −290 and −130 cm⁻¹.     

Utilization of blue-green light by chlorosomes from the photosynthetic bacterium Chloroflexus aurantiacus: Ultrafast excitation energy conversion and transfer

Chlorosomes of photosynthetic green bacteria are unique molecular assemblies providing efficient light harvesting followed by multi-step transfer of excitation energy to reaction centers. In each chlorosome, 10⁴–10⁵ bacteriochlorophyll (BChl) c/d/e molecules are organized by self-assembly into high-ordered aggregates. We studied the early-time dynamics of the excitation energy flow and energy conversion in chlorosomes isolated from Chloroflexus (Cfx.) aurantiacus bacteria by pump-probe spectroscopy with 30-fs temporal resolution at room temperature. Both the S₂ state of carotenoids (Cars) and the Soret states of BChl c were excited at ~490 nm, and absorption changes were probed at 400–900 nm. A global analysis of spectroscopy data revealed that the excitation energy transfer (EET) from Cars to BChl c aggregates occurred within ~100 fs, and the Soret → Q energy conversion in BChl c occurred faster within ~40 fs. This conclusion was confirmed by a detailed comparison of the early exciton dynamics in chlorosomes with different content of Cars. These processes are accompanied by excitonic and vibrational relaxation within 100–270 fs. The well-known EET from BChl c to the baseplate BChl a proceeded on a ps time-scale. We showed that the S₁ state of Cars does not participate in EET. We discussed the possible presence (or absence) of an intermediate state that might mediates the Soret → Q_y internal conversion in chlorosomal BChl c. We discussed a possible relationship between the observed exciton dynamics and the structural heterogeneity of chlorosomes.     

Boosting Oxygen Evolution Kinetics by Mn–N–C Motifs with Tunable Spin State for Highly Efficient Solar‐Driven Water Splitting

Solar‐driven water splitting is in urgent need for sustainable energy research, for which accelerating oxygen evolution kinetics along with charge migration is the key issue. Herein, Mn³⁺ within π‐conjugated carbon nitride (C₃N₄) in form of Mn–N–C motifs is coordinated. The spin state (e_g orbital filling) of Mn centers is regulated by controlling the bond strength of Mn–N. It is demonstrated that Mn serves as intrinsic oxygen evolution reaction (OER) site and the kinetics is dependent on its spin state with an optimized e_g occupancy of ≈0.95. Specifically, the governing role of e_g occupancy originates from the varied binding strength between Mn and OER intermediates. Benefiting from the rapid spin state‐mediated OER kinetics, as well as extended optical absorption (to 600 nm) and accelerated charge separation by intercalated metal‐to‐ligand state, Mn–C₃N₄ stoichiometrically splits pure water with H₂ production rate up to 695.1 µmol g^?1 h^?1 under simulated sunlight irradiation (AM1.5), and achieves an apparent quantum efficiency of 4.0% at 420 nm, superior to most solid‐state based photocatalysts to date. This work for the first time correlates photocatalytic redox kinetics with the spin state of active sites, and suggests a nexus between photocatalysis and spin theory.     

Temperature-dependent conformation change in spin-labeled hemoglobin

Hemoglobin was spin labeled at β-93(F9)-cysteine with N-oxy-2,2,6,6-tetramelhylpiperidinylmaleimide. The inward shift of the high-field hyperfine line (ΔH_XXX) position in the ESR spectra of the Spin label was measured aS a function of temperature. One can expect that an abrupt change in the microenvironment around the tightly bound spin label will be reflected in the function ΔH_XXX(T) as a discontinuity (break point). This was shown for aquo-, azido-. nitro- and oxyhemoglobin derivatives. The presented results suggest that the microenvironment around the tightly hound spin label in those methemoglobin derivatives that exhibit the mixed-spin state of the heme iron is prone to an abrupt change above a certain ligand-specific temperature. The change in microenvironment of the spin label is probably due to a temperature-dependent change in the tertiary structure of the protein.     

Charge separation in photosynthesis via a spin exchange coupling mechanism

A new mechanism for the primary photoinduced charge separation in photosynthesis is proposed. It involves as a real intermediate between the excited special pair state P^* and the primary charge separated state P⁺ H_L ^– a trip-trip-singlet B^T B_L ^T, which consists of a triplet on the dimer P and a further triplet on the monomer B_L. Both combine to a singlet. The electron transfer is caused by spin exchange couplings. The transient spectrum of the short lived intermediate, formerly taken as evidence for the charge transfer state P⁺ B_L ^–, is reinterpreted as a transient excitation of this trip-trip singlet. Received: 2 June 1997 / Accepted: 18 July 1997     

Density functional theory study of small nickel clusters

The stable geometries and atomization energies for the clusters Ni _n (n = 2–5) are predicted with all-electron density functional theory (DFT), using the BMK hybrid functional and a Gaussian basis set. Possible isomers and several spin states of these nickel clusters are considered systematically. The ground spin state and the lowest energy isomers are identified for each cluster size. The results are compared to available experimental and other theoretical data. The molecular orbitals of the largest cluster are plotted for all spin states. The relative stabilities of these states are interpreted in terms of superatom orbitals and no-pair bonding.     

The Nature of the Intramolecular Charge Transfer State in Peridinin

Experimental and theoretical evidence is presented that supports the theory that the intramolecular charge transfer (ICT) state of peridinin is an evolved state formed via excited-state bond-order reversal and solvent reorganization in polar media. The ICT state evolves in <100 fs and is characterized by a large dipole moment (∼35 D). The charge transfer character involves a shift of electron density within the polyene chain, and it does not involve participation of molecular orbitals localized in either of the β-rings. Charge is moved from the allenic side of the polyene into the furanic ring region and is accompanied by bond-order reversal in the central portion of the polyene chain. The electronic properties of the ICT state are generated via mixing of the “1¹B_u⁺” ionic state and the lowest-lying “2¹A_g^–” covalent state. The resulting ICT state is primarily ¹B_u⁺-like in character and exhibits not only a large oscillator strength but an unusually large doubly excited character. In most solvents, two populations exist in equilibrium, one with a lowest-lying ICT ionic state and a second with a lowest-lying “2¹A_g^–” covalent state. The two populations are separated by a small barrier associated with solvent relaxation and cavity formation.     

Backbone NMR assignments of a topologically knotted protein in urea-denatured state

YbeA is a 3-methylpseudoridine methyltransferase from Escherichia coli that forms a stable homodimer in solution. It is one of the deeply trefoil 3₁ knotted proteins, of which the knot encompasses the C-terminal helix that threads through a long loop. Recent studies on the knotted protein folding pathways using YbeA have suggested that the protein knot remains present under chemically denaturing conditions. Here, we report ¹H, ¹³C and ¹⁵N chemical shift assignments for urea-denatured YbeA, which will serve as the basis for further structural characterisations using solution state NMR spectroscopy with paramagnetic spin labeled and partial alignment media.     

Characterization of chlorophyll fluorescence quenching in chloroplasts by fluorescence spectroscopy at 77 K I. ΔpH-dependent quenching

The nature of the light-induced ΔpH-dependent decline of chlorophyll a fluorescence in intact and broken spinach chloroplasts was investigated. Fluorescence spectra at 77 K of chloroplasts frozen in the low-fluorescent (high ΔpH) state showed increased ratios of the band peak at 735 nm (Photosystem (PS) I fluorescence) to the peak at 695 nm (PS II fluorescence). The increase in the $\text{F}{}_{735}\text{F}{}_{695}$ ratio at 77 K was related to the extent of fluorescence quenching at room temperature. Normalization of low-temperature spectra with fluorescein as an internal standard revealed a lowering of F₆₉₅ that was not accompanied by an increase in F₇₃₅: preillumination before freezing decreased both F₆₉₅ and, to a lesser extent, F₇₃₅ in the spectra recorded at 77 K. Fluorescence induction of chloroplasts frozen in the low-fluorescent state showed a markedly decreased variable fluorescence (F_v) of PS II, but no concomitant increase in initial fluorescence (F₀) of PS I. Thus, the buildup of a proton gradient at the thylakoid membrane, as reflected by fluorescence quenching at room temperature, affects low-temperature fluorecence emission in a manner entirely different from the effect of removal of Mg²⁺, which is thought to alter the distribution of excitation energy in favor of PS I. The ΔpH-dependent quenching therefore cannot be caused by such change in energy distribution and is suggested to reflect increased thermal deactivation.     

Origin of the intrinsic rigidity of DNA

The intrinsic rigidities of DNA and RNA helices are generally thought to arise from some combination of vertical base-stacking interactions and intra-helix phosphate–phosphate charge repulsion; however, the relative contributions of these two types of interaction to helix rigidity have not been quantified. To address this issue, we have measured the rotational decay times of a ‘gapped-duplex’ DNA molecule possessing a central, single-stranded region, dT₂₄, before and after addition of the free purine base, N⁶-methyladenine (^meA). Upon addition of ^meA, the bases pair with the T residues, forming a continuous stack within the gap region. Formation of the gapped duplex is accompanied by a nearly 2-fold increase in decay time, to values that are indistinguishable from the full duplex control for monovalent salt concentrations up to 90 mM. These results indicate that at least 90% of the rigidity of the dT_n–dA_n homopolymer derives from base pair stacking effects, with phosphate–phosphate interactions contributing relatively little to net helix rigidity at moderate salt concentrations.     

DFT study of the intrinsic conformations of [2Fe-2S-4(SCH3)] clusters and their influence on exchange coupling

We have determined the equilibrium conformations of the diiron(III) cluster [2Fe-2S-4(SCH₃)]²⁻ using density functional theory. The conformers have dihedral Fe-Fe-S-C angles of ∼0° and ±120°. The relative energies of the conformers can be accurately parameterized with a small number of side-chain repulsion parameters. Of the 17 conformers identified on the basis of the ideal values for the dihedrals, 10 conformers are stable in both the ferromagnetic and broken symmetry state for the cluster. The exchange coupling constants for the seven energetically lowest conformers are predicted to belong to a narrow range, 150 cm⁻¹ ? J ? 178 cm⁻¹. The cluster conformers found in proteins do not coincide with any of the intrinsic ones, due to distortion of one of the dihedral angles under the influence of the protein scaffold.