Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct.

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.

Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM.

Solvent effects on 31P-NMR parameters for triphenylphosphine oxide and triphenylphosphine in chloroform have been extensively investigated by testing different solvation models. The solvent is described implicitly, mixed implicitly/explicitly, and using full explicit models. Polarizable continuum model (PCM), molecular dynamic (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to disclose the effects of solute/solvent interactions and, more generally, the role of the embedding in NMR simulations. The results show the beneficial effect of carrying out QM/MM optimizations on top of geometries directly extracted from classical MD simulations, used to ensure representative conformational sampling. The nuclear shielding convergence has been tested against a different number of snapshots and with the inclusion of solvent shells into the QM region. An automated MD//QM/MM//GIAO protocol, implemented in the COBRAMM package, is here proposed and tested on trimethyl phosphite showing that our approach boosts the convergence of nuclear shielding satisfactorily. The present work aims to be a stepping-stone to assess proper QM/MM computational strategies in simulating chemical shifts in non-homogeneous systems like supramolecular and biological systems.

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter.

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.

Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size.

We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.

Connected Component Analysis of Dynamical Perturbation Contact Networks.

Describing protein dynamical networks through amino acid contacts is a powerful way to analyze complex biomolecular systems. However, due to the size of the systems, identifying the relevant features of protein-weighted graphs can be a difficult task. To address this issue, we present the connected component analysis (CCA) approach that allows for fast, robust, and unbiased analysis of dynamical perturbation contact networks (DPCNs). We first illustrate the CCA method as applied to a prototypical allosteric enzyme, the imidazoleglycerol phosphate synthase (IGPS) enzyme from Thermotoga maritima bacteria. This approach was shown to outperform the clustering methods applied to DPCNs, which could not capture the propagation of the allosteric signal within the protein graph. On the other hand, CCA reduced the DPCN size, providing connected components that nicely describe the allosteric propagation of the signal from the effector to the active sites of the protein. By applying the CCA to the IGPS enzyme in different conditions, i.e., at high temperature and from another organism (yeast IGPS), and to a different enzyme, i.e., a protein kinase, we demonstrated how CCA of DPCNs is an effective and transferable tool that facilitates the analysis of protein-weighted networks.

Quantum-Classical Protocol for Efficient Characterization of Absorption Lineshape and Fluorescence Quenching upon Aggregation: The Case of Zinc Phthalocyanine Dyes.

A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.

Characterizing Counterion-Dependent Aggregation of Rhodamine B by Classical Molecular Dynamics Simulations.

The aggregation in a solution of charged dyes such as Rhodamine B (RB) is significantly affected by the type of counterion, which can determine the self-assembled structure that in turn modulates the optical properties. RB aggregation can be boosted by hydrophobic and bulky fluorinated tetraphenylborate counterions, such as F5TPB, with the formation of nanoparticles whose fluorescence quantum yield (FQY) is affected by the degree of fluorination. Here, we developed a classical force field (FF) based on the standard generalized Amber parameters that allows modeling the self-assembling process of RB/F5TPB systems in water, consistent with experimental evidence. Namely, the classical MD simulations employing the re-parametrized FF reproduce the formation of nanoparticles in the RB/F5TPB system, while in the presence of iodide counterions, only RB dimeric species can be formed. Within the large, self-assembled RB/F5TPB aggregates, the occurrence of an H-type RB-RB dimer can be observed, a species that is expected to quench RB fluorescence, in agreement with the experimental data of FQY. The outcome provides atomistic details on the role of the bulky F5TPB counterion as a spacer, with the developed classical FF representing a step towards reliable modeling of dye aggregation in RB-based materials.

Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase.

Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced selectivity and protection against overdosage. However, we need to better understand allosteric mechanisms in order to fully harness their potential in drug discovery. In this study, molecular dynamics simulations and nuclear magnetic resonance spectroscopy are used to investigate how increases in temperature affect allostery in imidazole glycerol phosphate synthase. Results demonstrate that temperature increase triggers a cascade of local amino acid-to-amino acid dynamics that remarkably resembles the allosteric activation that takes place upon effector binding. The differences in the allosteric response elicited by temperature increase as opposed to effector binding are conditional to the alterations of collective motions induced by either mode of activation. This work provides an atomistic picture of temperature-dependent allostery, which could be harnessed to more precisely control enzyme function.

Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis.

Emerging SARS-CoV-2 variants raise concerns about our ability to withstand the Covid-19 pandemic, and therefore, understanding mechanistic differences of those variants is crucial. In this study, we investigate disparities between the SARS-CoV-2 wild type and five variants that emerged in late 2020, focusing on the structure and dynamics of the spike protein interface with the human angiotensin-converting enzyme 2 (ACE2) receptor, by using crystallographic structures and extended analysis of microsecond molecular dynamics simulations. Dihedral angle principal component analysis (PCA) showed the strong similarities in the spike receptor binding domain (RBD) dynamics of the Alpha, Beta, Gamma, and Delta variants, in contrast with those of WT and Epsilon. Dynamical perturbation networks and contact PCA identified the peculiar interface dynamics of the Delta variant, which cannot be directly imputable to its specific L452R and T478K mutations since those residues are not in direct contact with the human ACE2 receptor. Our outcome shows that in the Delta variant the L452R and T478K mutations act synergistically on neighboring residues to provoke drastic changes in the spike/ACE2 interface; thus a singular mechanism of action eventually explains why it dominated over preceding variants.

Insight on Chirality Encoding from Small Thiolated Molecule to Plasmonic Au@Ag and Au@Au Nanoparticles.

Chiral plasmonic nanomaterials exhibiting intense optical activity are promising for numerous applications. In order to prepare those nanostructures, one strategy is to grow metallic nanoparticles in the presence of chiral molecules. However, in such approach the origin of the observed chirality remains uncertain. In this work, we expand the range of available chiral plasmonic nanostructures and we propose another vision of the origin of chirality in such colloidal systems. For that purpose, we investigated the synthesis of two core-shell Au@Ag and Au@Au systems built from gold nanobipyramid cores, in the presence of cysteine. The obtained nanoparticles possess uniform shape and size and show plasmonic circular dichroism in the visible range, and were characterized by electron microscopy, circular dichroism, and UV-vis-NIR spectroscopy. Opto-chiral responses were found to be highly dependent on the morphology and the plasmon resonance. It revealed (i) the importance of the anisotropy for Au@Au nanoparticles and (ii) the role of the multipolar modes for Au@Ag nanoparticles on the way to achieve intense plasmonic circular dichroism. The role of cysteine as shaping agent and as chiral encoder was particularly evaluated. Our experimental results, supported by theoretical simulations, contrast the hypothesis that chiral molecules entrapped in the nanoparticles determine the chiral properties, highlighting the key role of the outmost part of the nanoparticles shell on the plasmonic circular dichroism. Along with these results, the impact of enantiomeric ratio of cysteine on the final shape suggested that the presence of a chiral shape or chiral patterns should be considered.

Modelling quenching mechanisms of disordered molecular systems in the presence of molecular aggregates.

Exciton density dynamics recorded in time-resolved spectroscopic measurements is a useful tool to recover information on energy transfer (ET) processes that can occur at different timescales, up to the ultrafast regime. Macroscopic models of exciton density decays, involving both direct Förster-like ET and diffusion mechanisms for exciton-exciton annihilation, are largely used to fit time-resolved experimental data but generally neglect contributions from molecular aggregates that can work as quenching species. In this work, we introduce a macroscopic model that includes contributions from molecular aggregate quenchers in a disordered molecular system. As an exemplifying case, we considered a homogenous distribution of rhodamine B dyes embedded in organic nanoparticles to set the initial parameters of the proposed model. The influence of such model parameters is systematically analysed, showing that the presence of molecular aggregate quenchers can be monitored by evaluating the exciton density long time decays. We showed that the proposed model can be applied to molecular systems with ultrafast decays, and we anticipated that it could be used in future studies for global fitting of experimental data with potential support from first-principles simulations.

Distinct allosteric pathways in imidazole glycerol phosphate synthase from yeast and bacteria.

Understanding the relationship between protein structures and their function is still an open question that becomes very challenging when allostery plays an important functional role. Allosteric proteins, in fact, exploit different ranges of motions (from sidechain local fluctuations to long-range collective motions) to effectively couple distant binding sites, and of particular interest is whether allosteric proteins of the same families with similar functions and structures also necessarily share the same allosteric mechanisms. Here, we compared the early dynamics initiating the allosteric communication of a prototypical allosteric enzyme from two different organisms, i.e., the imidazole glycerol phosphate synthase (IGPS) enzymes from the thermophilic bacteria and the yeast, working at high and room temperatures, respectively. By combining molecular dynamics simulations and network models derived from graph theory, we found rather distinct early allosteric dynamics in the IGPS from the two organisms, involving significatively different allosteric pathways in terms of both local and collective motions. Given the successful prediction of key allosteric residues in the bacterial IGPS, whose mutation disrupts its allosteric communication, the outcome of this study paves the way for future experimental studies on the yeast IGPS that could foster therapeutic applications by exploiting the control of IGPS enzyme allostery.

Tracking excited state decay mechanisms of pyrimidine nucleosides in real time.

DNA owes its remarkable photostability to its building blocks-the nucleosides-that efficiently dissipate the energy acquired upon ultraviolet light absorption. The mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy experiments with broad spectral coverage and state-of-the-art mixed quantum-classical dynamics with spectral signal simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. We track the wave packet motion from the Franck-Condon region to the conical intersections (CIs) with the ground state and observe spectral signatures of excited-state vibrational modes. 5mUrd exhibits an order of magnitude longer lifetime with respect to Urd due to the solvent reorganization needed to facilitate bulky methyl group motions leading to the CI. This activates potentially lesion-inducing dynamics such as ring opening. Involvement of the 1nπ* state is found to be negligible.

Elucidating the Activation Mechanism of AMPK by Direct Pan-Activator PF-739.

Adenosine monophosphate-activated protein kinase (AMPK) is a key energy sensor regulating the cell metabolism in response to energy supply and demand. The evolutionary adaptation of AMPK to different tissues is accomplished through the expression of distinct isoforms that can form up to 12 heterotrimeric complexes, which exhibit notable differences in the sensitivity to direct activators. To comprehend the molecular factors of the activation mechanism of AMPK, we have assessed the changes in the structural and dynamical properties of ß1- and ß2-containing AMPK complexes formed upon binding to the pan-activator PF-739. The analysis revealed the molecular basis of the PF-739-mediated activation of AMPK and enabled us to identify distinctive features that may justify the slightly higher affinity towards the ß1-isoform, such as the ß1-Asn111 to ß2-Asp111 substitution, which seems to be critical for modulating the dynamical sensitivity of ß1- and ß2 isoforms. The results are valuable in the design of selective activators to improve the tissue specificity of therapeutic treatment.

Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores.

Artificial biomimetic chromophore-protein complexes inspired by natural visual pigments can feature color tunability across the full visible spectrum. However, control of excited state dynamics of the retinal chromophore, which is of paramount importance for technological applications, is lacking due to its complex and subtle photophysics/photochemistry. Here, ultrafast transient absorption spectroscopy and quantum mechanics/molecular mechanics simulations are combined for the study of highly tunable rhodopsin mimics, as compared to retinal chromophores in solution. Conical intersections and transient fluorescent intermediates are identified with atomistic resolution, providing unambiguous assignment of their ultrafast excited state absorption features. The results point out that the electrostatic environment of the chromophore, modified by protein point mutations, affects its excited state properties allowing control of its photophysics with same power of chemical modifications of the chromophore. The complex nature of such fine control is a fundamental knowledge for the design of bio-mimetic opto-electronic and photonic devices.

On the origin of controlled anisotropic growth of monodisperse gold nanobipyramids.

We elucidate the crucial role of the cetyl trimethylammonium bromide (CTAB) surfactant in the anisotropic growth mechanism of gold nano-bipyramids, nano-objects with remarkable optical properties and high tunability. Atomistic molecular dynamics simulations predict different surface coverages of the CTAB (positively charged) heads and their (bromide) counterions as function of the gold exposed surfaces. High concentration of CTAB surfactant promotes formation of gold nanograins in solution that work as precursors for the smooth anisotropic growth of more elongated nano-bipyramidal objects. Nanobipyramids feature higher index facets with respect to nanorods, allowing higher CTAB coverages that stabilize their formation and leading to narrower inter-micelles channels that smooth down their anisotropic growth. Absorption spectroscopy and scanning electron microscopy confirmed the formation of nanograins and demonstrated the importance of surfactant concentration on driving the growth towards nano-bipyramids rather than nanorods. The outcome explains the formation of the monodisperse bipyramidal nano-objects, the origin of their controlled shapes and sizes along with their remarkable stability.

Heterometallic rhodium clusters as electron reservoirs: Chemical, electrochemical, and theoretical studies of the centered-icosahedral [Rh12E(CO)27]n- atomically precise carbonyl compounds.

In this paper, we present a comparative study of the redox properties of the icosahedral [Rh12E(CO)27]n- (n = 4 when E = Ge or Sn and n = 3 when E = Sb or Bi) family of clusters through in situ infrared spectroelectrochemistry experiments and density functional theory computational studies. These clusters show shared characteristics in terms of molecular structure, being all E-centered icosahedral species, and electron counting, possessing 170 valence electrons as predicted by the electron-counting rules, based on the cluster-borane analogy, for compounds with such metal geometry. However, in some cases, clusters of similar nuclearity, and beyond, may show multivalence behavior and may be stable with a different electron counting, at least on the time scale of the electrochemical analyses. The experimental results, confirmed by theoretical calculations, showed a remarkable electron-sponge behavior for [Rh12Ge(CO)27]4- (1), [Rh12Sb(CO)27]3- (3), and [Rh12Bi(CO)27]3- (4), with a cluster charge going from -2 to -6 for 1 and 3 and from -2 to -7 for cluster 4, making them examples of molecular electron reservoirs. The [Rh12Sn(CO)27]4- (2) derivative, conversely, presents a limited ability to exist in separable reduced cluster species, at least within the experimental conditions, while in the gas phase it appears to be stable both as a penta- and hexa-anion, therefore showing a similar redox activity as its congeners. As a fallout of those studies, during the preparation of [Rh12Sb(CO)27]3-, we were able to isolate a new species, namely, [Rh11Sb(CO)26]2-, which presents a Sb-centered nido-icosahedral metal structure possessing 158 cluster valence electrons, in perfect agreement with the polyhedral skeletal electron pair theory.

Polymerization Isomerism in Co-M (M = Cu, Ag, Au) Carbonyl Clusters: Synthesis, Structures and Computational Investigation.

The reaction of [Co(CO)4]- (1) with M(I) compounds (M = Cu, Ag, Au) was reinvestigated unraveling an unprecedented case of polymerization isomerism. Thus, as previously reported, the trinuclear clusters [M{Co(CO)4}2]- (M = Cu, 2; Ag, 3; Au, 4) were obtained by reacting 1 with M(I) in a 2:1 molar ratio. Their molecular structures were corroborated by single-crystal X-ray diffraction (SC-XRD) on isomorphous [NEt4][M{Co(CO)4}2] salts. [NEt4](3)represented the first structural characterization of 3. More interestingly, changing the crystallization conditions of solutions of 3, the hexanuclear cluster [Ag2{Co(CO)4}4]2- (5) was obtained in the solid state instead of 3. Its molecular structure was determined by SC-XRD as Na2(5)·C4H6O2, [PPN]2(5)·C5H12 (PPN = N(PPh3)2]+), [NBu4]2(5) and [NMe4]2(5) salts. 5 may be viewed as a dimer of 3 and, thus, it represents a rare case of polymerization isomerism (that is, two compounds having the same elemental composition but different molecular weights) in cluster chemistry. The phenomenon was further studied in solution by IR and ESI-MS measurements and theoretically investigated by computational methods. Both experimental evidence and density functional theory (DFT) calculations clearly pointed out that the dimerization process occurs in the solid state only in the case of Ag, whereas Cu and Au related species exist only as monomers.