Role for bound water and CH-pi aromatic interactions in photosynthetic electron transfer

Molecular duplexes featuring NH···N, CH···O and CH···π interactions in solid-state self-assembly of triazine-based compounds

Synthetic supramolecular structures constructed through the cooperative action of numerous non-covalent forces are highly desirable as models to unravel and understand the complexity of systems created in nature via self-assembly. Taking advantage of the low cost of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and the sequential nucleophilic substitution reactions with almost all types of nucleophiles, a series of six structurally related novel s-triazine derivatives 1-6 were synthesized and structurally characterized based on their physical, spectral and crystallographic data. The solid-state structures of all the six compounds showed intriguing and unique molecular duplexes featuring NH···N, CH···O and CH···π interactions. Careful analysis of different geometric parameters of the involved H-bonds indicates that they are linear, significant and are therefore responsible for guiding the three-dimensional structure of these compounds in the solid state. The prevalence of sextuple hydrogen bond array-driven molecular duplexes and the possibility of structural modifications on the s-triazine ring render these novel triazine derivatives 1-6 attractive as a platform to create heteroduplex constructs and their subsequent utility in the field of supramolecular chemistry and crystal engineering.

Intramolecular Noncovalent Carbon Bonding Interaction Stabilizes the cis Conformation in Acylhydrazones

Noncovalent carbon bonding, a recently explored σ-hole interaction, was hitherto supposed to be a weak and structure-guided interaction. Here, its role in the intramolecular stabilization of the cis conformation of the amide moiety in acylhydrazones is described. The calculations reveal an electron donation from the lone pair of the nitrogen atom to the empty antibonding C-N orbital [LP(N)→BD*(C-N)] with a concomitant stabilization energy of E⁽²⁾ =1.2 kcal mol^-1 .

Acceleration of the excitation decay in Photosystem I immobilized on glass surface

Femtosecond transient absorption was used to study excitation decay in monomeric and trimeric cyanobacterial Photosystem I (PSI) being prepared in three states: (1) in aqueous solution, (2) deposited and dried on glass surface (either conducting or non-conducting), and (3) deposited on glass (conducting) surface but being in contact with aqueous solvent. The main goal of this contribution was to determine the reason of the acceleration of the excitation decay in dried PSI deposited on the conducting surface relative to PSI in solution observed previously using time-resolved fluorescence (Szewczyk et al., Photysnth Res 132(2):111-126, 2017). We formulated two alternative working hypotheses: (1) the acceleration results from electron injection from PSI to the conducting surface; (2) the acceleration is caused by dehydration and/or crowding of PSI proteins deposited on the glass substrate. Excitation dynamics of PSI in all three types of samples can be described by three main components of subpicosecond, 3-5, and 20-26 ps lifetimes of different relative contributions in solution than in PSI-substrate systems. The presence of similar kinetic components for all the samples indicates intactness of PSI proteins after their deposition onto the substrates. The kinetic traces for all systems with PSI deposited on substrates are almost identical and they decay significantly faster than the kinetic traces of PSI in solution. We conclude that the accelerated excitation decay in PSI-substrate systems is caused mostly by dense packing of proteins.

CH-π hydrogen bonds in biological macromolecules

This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.

Polymer chain length, phosphoric acid doping and temperature dependence on structure and dynamics of an ABPBI [poly(2,5-benzimidazole)] polymer electrolyte membrane

The random orientations of BI units and the presence of free rotation around the single bond which connects two monomeric BI segments lead to minimal possibility of π–π interactions.

Homologous 1,3,5-triarylpyrazolines: synthesis, CH⋯π interactions guided self-assembly and effect of alkyloxy chain length on DNA binding properties

The synthesis, CH⋯π interactions-driven self-assembled structure and DNA binding properties (10⁵–10⁶M⁻¹binding constants) of new homologous 1,3,5-triaryl-2-pyrazolines are reported.

XH/π (X = C, Si) Interactions in Graphene and Silicene: Weak in Strength, Strong in Tuning Band Structures

The lack of a band gap has greatly hindered the applications of graphene in electronic devices. By means of dispersion-corrected density functional theory computations, we demonstrated that considerable CH/π interactions exist between graphene and its fully (graphane) or patterned partially (C4H) hydrogenated derivatives. Due to the equivalence breaking of two sublattices of graphene, a 90 meV band gap is opened in the graphene/C4H bilayer. The band gap can be further increased to 270 meV by sandwiching graphene between two C4H layers. By taking advantage of the similar SiH/π interactions, a 120 meV band gap also can be opened for silicene. Interestingly, the high carrier mobility of graphene/silicene can be well-preserved. Our theoretical results suggest a rather practical solution for gap opening of graphene and silicene, which would allow them to serve as field effect transistors and other nanodevices.

Tryptophan as a probe of photosystem I electron transfer reactions: a UV resonance Raman study

Photosystem I (PSI) is one of the two membrane-associated reaction centers involved in oxygenic photosynthesis. In photosynthesis, solar energy is converted to chemical energy in the form of a transmembrane charge separation. PSI oxidizes cytochrome c(6) or plastocyanin and reduces ferredoxin. In cyanobacterial PSI, there are 10 tryptophan residues with indole side chains located less than 10 A from the electron transfer cofactors. In this study, we apply pump-probe difference UV resonance Raman (UVRR) spectroscopy to acquire the spectrum of aromatic amino acids in cyanobacterial PSI. This UVRR technique allows the use of the tryptophan vibrational spectrum as a reporter for structural changes, which are linked to PSI electron transfer reactions. Our results show that photo-oxidation of the chlorophyll a/a' heterodimer, P(700), causes shifts in the vibrational frequencies of two or more tryptophan residues. Similar perturbations of tryptophan are observed when P(700) is chemically oxidized. The observed spectral frequencies suggest that the perturbed tryptophan side chains are only weakly or not hydrogen bonded and are located in an environment in which there is steric repulsion. The direction of the spectral shifts is consistent with an oxidation-induced increase in dielectric constant or a change in hydrogen bonding. To explain our results, the perturbation of tryptophan residues must be linked to a PSI conformational change, which is, in turn, driven by P(700) oxidation.

An altered mode of calcium coordination in methionine-oxidized calmodulin

Oxidation of methionine residues in calmodulin (CaM) lowers the affinity for calcium and results in an inability to activate target proteins fully. To evaluate the structural consequences of CaM oxidation, we used infrared difference spectroscopy to identify oxidation-dependent effects on protein conformation and calcium liganding. Oxidation-induced changes include an increase in hydration of alpha-helices, as indicated in the downshift of the amide I' band of both apo-CaM and Ca(2+)-CaM, and a modification of calcium liganding by carboxylate side chains, reflected in antisymmetric carboxylate band shifts. Changes in carboxylate ligands are consistent with the model we propose: an Asp at position 1 of the EF-loop experiences diminished hydrogen bonding with the polypeptide backbone, an Asp at position 3 forms a bidentate coordination of calcium, and an Asp at position 5 forms a pseudobridging coordination with a calcium-bound water molecule. The bidentate coordination of calcium by conserved glutamates is unaffected by oxidation. The observed changes in calcium ligation are discussed in terms of the placement of methionine side chains relative to the calcium-binding sites, suggesting that varying sensitivities of binding sites to oxidation may underlie the loss of CaM function upon oxidation.

Light-induced dynamics in photosystem I electron transfer

Protein dynamics are likely to play important, regulatory roles in many aspects of photosynthetic electron transfer, but a detailed description of these coupled protein conformational changes has been unavailable. In oxygenic photosynthesis, photosystem I catalyzes the light-driven oxidation of plastocyanin or cytochrome c and the reduction of ferredoxin. A chlorophyll (chl) a/a' heterodimer, P(700), is the secondary electron donor, and the two P(700) chl, are designated P(A) and P(B). We used specific chl isotopic labeling and reaction-induced Fourier-transform infrared spectroscopy to assign chl keto vibrational bands to P(A) and P(B). In the cyanobacterium, Synechocystis sp. PCC 6803, the chl keto carbon was labeled from (13)C-labeled glutamate, and the chl keto oxygen was labeled from (18)O(2). These isotope-based assignments provide new information concerning the structure of P(A)(+), which is found to give rise to two chl keto vibrational bands, with frequencies at 1653 and 1687 cm(-1). In contrast, P(A) gives rise to one chl keto band at 1638 cm(-1). The observation of two P(A)(+) keto frequencies is consistent with a protein relaxation-induced distribution in P(A)(+) hydrogen bonding. These results suggest a light-induced conformational change in photosystem I, which may regulate the oxidation of soluble electron donors and other electron-transfer reactions. This study provides unique information concerning the role of protein dynamics in oxygenic photosynthesis.

Solvent-induced changes in photochemical activity and conformation of photosystem I particles by glycerol

It has been shown that a large number of water molecules coordinate with the pigments and subunits of photosystem I (PSI); however, the function of these water molecules remains to be clarified. In this study, the photosynthetic properties of PSI from spinach were investigated using different spectroscopic and activity measurements under conditions of decreasing water content caused by increasing concentrations of glycerol. The results show that glycerol addition caused pronounced changes in the photochemical activity of PSI particles. At low concentrations (<60%, v/v), glycerol stimulated the rate of oxygen uptake in PSI particles, while higher concentrations of glycerol cause inhibition of PSI activity. The capacity of P700 photooxidation also increased with glycerol concentrations lower than 60%. In contrast, this capacity decreased at higher glycerol concentrations. On the other hand, glycerol addition considerably affected the distribution of the bulk and red antenna chlorophyll (Chl) forms or states, with the population of red-shifted Chl forms augmented with increasing glycerol. In addition, glycerol-treated PSI particles showed a blue shift of the tryptophan fluorescence emission maximum and an increase in their capacity to bind the hydrophobic probe 1-anilino-8-naphthalene sulfonate, indicating a more non-polar environment for tryptophan residues and increased exposure of hydrophobic surfaces.