Study of Photoselectivity in Linear Conjugated Chromophores Using the XMS-CASPT2 Method.

Photoisomerization, the structural alteration of molecules upon absorption of light, is crucial for the function of biological chromophores such as retinal in opsins, proteins vital for vision and other light-sensitive processes. The intrinsic selectivity of this isomerization process (i.e.

Ultrafast structural changes direct the first molecular events of vision.

Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs). A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear.

Dynamics and mechanism of a light-driven chloride pump.

Chloride transport by microbial rhodopsins is an essential process for which molecular details such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport have remained elusive. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride-pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion-binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport.

Π-Stacking in Heterodimers of Propargylbenzene with (Fluoro)phenylacetylenes.

The heterodimers of propargylbenzene (PrBz) with phenylacetylene (PHA) and monosubstituted fluorophenylacetylenes (FPHAs) were investigated using electronic and vibrational spectroscopic methods. The vibrational spectra in the acetylenic C-H stretching region show a marginal shift (0-4 cm) upon dimer formation, which suggests minimal perturbation of the acetylenic group. The M06-2X/aug--pVDZ calculations indicate that the π-stacked structures are the most stable, followed by other structures.

Correction: Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2.

Correction for 'Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2' by Aditya G. Rao et al., Phys.

Histidine protonation controls structural heterogeneity in the cyanobacteriochrome AnPixJg2.

Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. These photochemical properties make them an attractive target for biotechnological applications.

Frontiers in Multiscale Modeling of Photoreceptor Proteins.

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.

Dipole Moment Propels π-Stacking of Heterodimers of Fluorophenylacetylenes.

Electronic and vibrational spectroscopic investigations in combination with quantum chemical calculations were carried out to probe the formation of four sets of heterodimers of phenylacetylene with 2-fluorohenylacetylene, 3-fluorophenylacetylene, 4-fluorophenylacetylene, and 2,6-difluorophenylacetylene. The interaction of phenylacetylene with fluorophenylacetylenes leads to marginal (2-9 cm) red-shifts in the acetylenic C-H stretching frequencies of fluorophenylacetylenes, which suggests that constituent monomers are minimally perturbed in the heterodimer. On the other hand, the density-functional-theory-based calculations indicate that π-stacked structures outweigh other structures incorporating C-H···π and C-H···F interactions by about 8 kJ mol or more.

π-Stacking Driven Aggregation and Folding of Squaramides.

Competing noncovalent interactions play a pivotal role in the folding and assembly of three-dimensional structures, especially in flexible molecules. Calculations using density functional theory reveal that two squaramide rings aggregate to form a slipped antiparallel π-stacked dimer with high propensity. This π-π stacking interaction is used to design foldamers in which the squaramides are tethered by a simple methylene bridge, and consequently, the structure folds on to itself incorporating a "turn" element.

Modern quantum chemistry with [Open]Molcas.

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein.

ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter.

Electrostatics and Dispersion in X-H···Y (X = C, N, O; Y = N, O) Hydrogen Bonds and Their Role in X-H Vibrational Frequency Shifts.

The frequency shifts of donor stretching vibration in X-H···Y (X = C, N, O; Y = N, O) hydrogen-bonded complexes of phenylacetylene, indole, and phenol are linearly correlated with the electrostatic component of the interaction energy. This linear correlation suggests that the electrostatic component, which is the first-order perturbative correction to the stabilization energy, is essentially localized on the X-H group. The linear correlation suggests that the electrostatic tuning rate, which is a measure of the X-H oscillator to undergo shifts upon hydrogen bonding per unit increase in the electrostatic component of the stabilization energy, was found to be in the order of O-H > N-H > C-H.

π-Stacked Dimers of Fluorophenylacetylenes: Role of Dipole Moment.

The homodimers of singly fluorine-substituted phenylacetylenes were investigated using electronic and vibrational spectroscopic methods in combination with density functional theory calculations. The IR spectra in the acetylenic C-H stretching region show a marginal red shift for the dimers relative to the monomers. Further, the marginal red shifts indicate that the acetylenic group in all the dimers is minimally perturbed relative to the corresponding monomer.

Elusive Double-Eight-Ring Zeolitic Secondary Building Unit.

The double-eight-ring (D8R), an elusive secondary building unit of zeolites, has been stabilized for the first time, both in solution and solid-state. The present study further establishes that any of the three double-ring building blocks of zeolites, viz. D4R, D6R and D8R ([ArPOZn(L)] (n = 4, 6 or 8)), can be preferentially isolated (over the other two) through a careful choice of metal source, aryl phosphate and ancillary ligand, apart from maintaining a meticulous control on the reaction conditions.

Internal electric fields in small water clusters [(H2O)n; n = 2-6].

The electric field experienced by a water molecule within a water cluster depends on its position relative to the rest of the water molecules. The stabilization energies and the red-shifts in the donor O-H stretching vibrations in the water clusters increase with the cluster size concomitant with the increase in the electric field experienced by the donor O-H of a particular water molecule due to the hydrogen bonding network. The red-shifts in O-H stretching frequencies show a spread of about ±100 cm(-1) against the corresponding electric fields.

Spectroscopic and Ab Initio Investigation of C-H⋅⋅⋅N Hydrogen-Bonded Complexes of Fluorophenylacetylenes: Frequency Shifts and Correlations.

The C-H⋅⋅⋅N hydrogen-bonded complexes of several fluorophenyacetylenes with ammonia and methylamine were characterized by a redshift in the acetylenic C-H stretching vibration of the phenylacetylene moiety. These redshifts were linearly correlated with the stabilization energies calculated at the CCSD(T)/CBS//MP2-aug-cc-pVDZ level. Analysis of various components of the interaction energy indicated that the observed redshifts were weakly correlated with the electrostatic component.

Three-Fold C 3-Symmetric Off-On Fluorescent Chemo-Sensors for Fluoride.

Three novel C 3-symmetric tris-salicylaldimine Schiff base based "off-on" fluorescence sensors have been designed and synthesized. The synthetic approach involves a simple imine bond (C = N) formation between 1,3,5-tris(4'-aminophenyl)benzene (TAPB) and 3,5-substituted salicylaldehydes. The presence of salicylaldehyde units on periphery of the tris-salicylaldimine Schiff bases masks the fluorescence of TAPB core.

Octanuclear zinc phosphates with hitherto unknown cluster architectures: ancillary ligand and solvent assisted structural transformations thereof.

Structural variations in zinc phosphate cluster chemistry have been achieved through a careful selection of phosphate ligand, ancillary ligand, and solvent medium. The use of 4-haloaryl phosphates (X-dippH2) as phosphate source in conjunction with 2-hydroxypyridine (hpy) ancillary ligand in acetonitrile solvent resulted in the isolation of the first examples of octameric zinc phosphates [Zn8(X-dipp)8(hpy)4(CH3CN)2(H2O)2]·4H2O (X = Cl 2, Br 3) and not the expected tetranuclear D4R cubane clusters. Use of 2,3-dihydroxypyridine (dhpy) as ancillary ligand, under otherwise similar reaction conditions with the same set of phosphate ligands and solvent, resulted in isolation of another type of octanuclear zinc phosphate clusters {[(Zn8(X-dipp)4(X-dippH)4(dhpyH)4(dhpyH2)2(H2O)2]·2solvent} (X = Cl, solvent = MeCN 4; Br, solvent = H2O 5), as the only isolated products.

The propargylbenzene dimer: C-H···π assisted π-π stacking.

The propargylbenzene dimer was investigated using mass selected electronic and infrared spectroscopy in combination with quantum chemical calculations. The IR spectrum in the acetylenic C-H stretching region indicates that the two propargylbenzene units in the dimer are in an almost identical environment. The stabilization energies calculated at various levels of theory predict that the anti-parallel structure is the most stable isomer.

Selective fluorescence sensing of polynitroaromatic explosives using triaminophenylbenzene scaffolds.

A supramolecular fluorophore, 1,3,5-tris(4'-aminophenyl)benzene (TAPB), selectively senses polynitroaromatic compounds (PNAC), viz. 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), picric acid (PA), m-dinitrobenzene (m-DNB) and p-dinitrobenzene (p-DNB) through donor-acceptor complexation. Steady-state and time resolved fluorescence measurements indicate predominantly static quenching of the TAPB fluorophore with TNT, DNT, m-DNB and p-DNB.