Stabilization of Charge-Transfer Excited States in Biological Systems: A Computational Focus on the Special Pair in Photosystem II Reaction Centers.

Charge-transfer (CT) excited states play an important role in many biological processes. However, many computational approaches often inadequately address the equilibration effects of nuclear and environmental degrees of freedom on these states. One prominent example of systems in which CT states are of utmost importance is reaction centers (RC) in photosystems. Here we use a multiscale approach combined with time-dependent density functional theory to explore the lowest CT excited state of the special pair PD1-PD2 in the Photosystem II-RC of a cyanobacterium. We find that the nonequilibrium CT excited state resides near the Soret band, making an exciton the lowest-energy excited state. However, accounting for nuclear and state-specific dielectric equilibration along the CT potential energy surface (PES), the CT state PD1--PD2+ stabilizes energetically below the excitonic state. This underscores the crucial role of state-specific solvation in mapping the PES of CT states, as demonstrated in a simplified dimer model.

Factor H-related protein 1 promotes complement-mediated opsonization of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is an important human opportunistic pathogen responsible for a wide range of infections. The complement system is the main early host defense mechanism to control these infections. P. aeruginosa counteracts complement attack by binding Factor H (FH), a complement regulator that inactivates C3b, preventing the formation of the C3-convertase and complement amplification on the bacterial surface. Factor H-related proteins (FHRs) are a group of plasma proteins evolutionarily related to FH that have been postulated to interfere in this bacterial mechanism of resisting complement. Here, we show that FHR-1 binds to P. aeruginosa via the outer membrane protein OprG in a lipopolysaccharide (LPS) O antigen-dependent manner. Binding assays with purified components or with FHR-1-deficient serum supplemented with FHR-1 show that FHR-1 competes with FH for binding to P. aeruginosa. Blockage of FH binding to C3b deposited on the bacteria reduces FH-mediated cofactor activity of C3b degradation, increasing the opsonization of the bacteria and the formation of the potent chemoattractant C5a. Overall, our findings indicate that FHR-1 is a host factor that promotes complement activation, facilitating clearance of P. aeruginosa by opsonophagocytosis.

Resolving the Puzzle of Charge Carrier Lifetime in ZnO by Revisiting the Role of Oxygen Vacancy.

Zinc oxide (ZnO) is a wide bandgap prototypical n-type semiconductor due to the presence of intrinsic oxygen vacancies (VO). The VO can readily transfer to the most energetically favorable +2 charged VO (VO2+) by losing two electrons mediated by the metastable VO1+ defect. Nevertheless, the influence of charged VO on the charge dynamics in ZnO and the underlying mechanisms remain elusive. By performing nonadiabatic molecular dynamics simulations of the charge trapping and recombination processes, we show that both VO1+ and VO2+ slow down the nonradiative electron-hole recombination via assisted defect states and, thus, extending charge carrier lifetime compared to pristine ZnO. Our study contributes to identifying the different recombination pathways that take place in VO1+ and VO2+ of n-type ZnO systems, providing useful guidance for designing high-performance ZnO-based devices.

Sub-ppm Methane Detection with Mid-Infrared Slot Waveguides.

Hybrid integration of photonic chips with electronic and micromechanical circuits is projected to bring about miniature, but still highly accurate and reliable, laser spectroscopic sensors for both climate research and industrial applications. However, the sensitivity of chip-scale devices has been limited by immature and lossy photonic waveguides, weak light-analyte interaction, and etalon effects from chip facets and defects. Addressing these challenges, we present a nanophotonic waveguide for methane detection at 3270.4 nm delivering a limit of detection of 0.3 ppm, over 2 orders of magnitude lower than the state-of-the-art of on-chip spectroscopy. We achieved this result with a Si slot waveguide designed to maximize the light-analyte interaction, while special double-tip fork couplers at waveguide facets suppress spurious etalon fringes. We also study and discuss the effect of adsorbed humidity on the performance of mid-infrared waveguides around 3 µm, which has been repeatedly overlooked in previous reports.

Twisting Aromaticity and Photoinduced Dynamics in Hexapole Helicenes.

Curved aromatic molecules are attractive electronic materials, where an additional internal strain uniquely modifies their structure, aromaticity, dynamics, and optical properties. Helicenes are examples of such twisted conjugated systems. Herein, we analyze the photoinduced dynamics in different stereoisomers of a hexapole helicene by using nonadiabatic excited-state molecular dynamics simulations. We explore how changes in symmetry and structural distortion modulate the intramolecular energy redistribution. We find that distinct helical assembly leads to different rigid distorted structures that in turn impact the nonradiative energy relaxation and ultimately formation of the self-trapped exciton. Subsequently, the value of the twisting angles relative to the central triphenylene core structure controls the global molecular aromaticity and electronic localization during the internal conversion process. Our work sheds light on how the future synthesis of novel curved aromatic compounds can be directed to attain specific desired electronic properties through the modulation of their twisted aromaticity.

Evidence of H/D Exchange within Metal-Adducted Carbohydrates after Ion/Ion-Dissociation Reactions.

Tandem mass spectrometry (MS/MS) using fragmentation has become one of the most effective methods for gaining sequence and structural information on biomolecules. Ion/ion reactions are competitive reactions, where either proton transfer (PT) or electron transfer (ET) can occur from interactions between multiply charged cations and singly charged anions. Utilizing ion/ion reactions with fluoranthene has offered a unique method of fragment formation for the structural elucidation of biomolecules. Fluoranthene is considered an ideal anion reagent because it selectively causes electron-transfer dissociation (ETD) and minimizes PT when interacting with peptides. However, limited investigations have sought to understand how fluoranthene─the primary, commercially available anion reagent─interacts with other biomolecules. Here, we apply deuterium labeling to investigate ion/ion reaction mechanisms between fluoranthene and divalent, metal-adducted carbohydrates (Ca2+, Mg2+, Co2+, and Ni2+). Deuterium labeling of carbohydrates allowed us to observe evidence of hydrogen/deuterium exchange (HDX) occurring after ion/ion dissociation reactions. The extent of deuterium loss is dependent on several factors, including the physical properties of the metal ion and the fragment structure. Based on the deuterium labeling data, we have proposed ETD, PTD, and intermolecular PT─also described as HDX─mechanisms. This research provides a fundamental perspective of ion/ion and ion/molecule reaction mechanisms and illustrates properties that impact ion/ion and ion/molecule reactions for carbohydrates. Together, this could improve the capability to distinguish complex and heterogeneous biomolecules, such as carbohydrates.

NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations.

We present NEXMD version 2.0, the second release of the NEXMD (Nonadiabatic EXcited-state Molecular Dynamics) software package. Across a variety of new features, NEXMD v2.0 incorporates new implementations of two hybrid quantum-classical dynamics methods, namely, Ehrenfest dynamics (EHR) and the Ab-Initio Multiple Cloning sampling technique for Multiconfigurational Ehrenfest quantum dynamics (MCE-AIMC or simply AIMC), which are alternative options to the previously implemented trajectory surface hopping (TSH) method. To illustrate these methodologies, we outline a direct comparison of these three hybrid quantum-classical dynamics methods as implemented in the same NEXMD framework, discussing their weaknesses and strengths, using the modeled photodynamics of a polyphenylene ethylene dendrimer building block as a representative example. We also describe the expanded normal-mode analysis and constraints for both the ground and excited states, newly implemented in the NEXMD v2.0 framework, which allow for a deeper analysis of the main vibrational motions involved in vibronic dynamics. Overall, NEXMD v2.0 expands the range of applications of NEXMD to a larger variety of multichromophore organic molecules and photophysical processes involving quantum coherences and persistent couplings between electronic excited states and nuclear velocity.

Environmental surveillance of Pseudomonas aeruginosa in recreational waters in tourist facilities of the Balearic Islands, Spain (2016-2019).

BACKGROUND: Pseudomonas aeruginosa is a major opportunistic human pathogen commonly connected with recreational water activities. Spain is a tourist destination where most of the establishments have swimming pool. Nevertheless, the prevalence of P. aeruginosa in public swimming pools in our country is unknown. This works aimed to survey the P. aeruginosa presence in tourist Spanish recreational waters. METHOD: Tourist recreational water in hotels in the Balearic Islands were visited for four years (2016-2019). The levels of selected parameters were determined, and their correlation with P. aeruginosa contamination investigated. RESULTS: We evaluated 11,014 samples from 254 facilities. Unacceptable levels of at least one legislated parameter were detected in 30.7% of cases, implicating closure in 15.9%, being P. aeruginosa the leading cause of closure. The prevalence of the pathogen was 14.2%, with lower presence in outer swimming pools. Disinfectant levels influence P. aeruginosa contamination, and bromine-maintained pools were more often contaminated than those treated with chlorine. Prevalence remained constant over the years, although it increased in 2019. CONCLUSIONS: P. aeruginosa prevalence in our recreational waters is similar to other countries, and the contamination rates depend on the installations and type and disinfectant levels. Corrective measures are still needed to improve pathogen control.

Impact of the core on the inter-branch exciton exchange in dendrimers.

Organic dendrimers with π conjugated systems are capable of capturing solar energy as a renewable source for human use. Nonetheless, further study regarding the relationship between the structure and the energy transfer mechanism in these types of molecules is still necessary. In this work, nonadiabatic excited state molecular dynamics (NEXMD) were carried out to study the intra- and inter-branch exciton migration in two tetra-branched dendrimers, C(dSSB)4 and Ad(BuSSB)4, which differ in their respective carbon and adamantane core. Both systems undergo a ladder decay mechanism between excited states, with back-and-forth transitions between S1 and S2. Despite presenting very similar absorption-emission spectra, differences in the photoinduced energy relaxation are observed. The size of the core impacts the inter-branch energy exchange and transient exciton localization/delocalization, which ultimately condition the relative energy relaxation rates, being faster in Ad(BuSSB)4 with respect to C(dSSB)4. Nevertheless, the photoinduced processes lead to a progressive final exciton-self-trapping in one of the branches of both dendrimers, which is a desirable feature in organic photovoltaic applications. Our results can inspire the design of more efficient dendrimers with the desired magnitude of inter-branch exciton exchange and localization/delocalization according to changes in their core.

Vibrational Funnels for Energy Transfer in Organic Chromophores.

Photoinduced intramolecular energy transfers in multichromophoric molecules involve nonadiabatic vibronic channels that act as energy transfer funnels. They commonly take place through specific directions of motion dictated by the nonadiabatic coupling vectors. Vibrational funnels may support persistent coherences between electronic states and sometimes delineate the presence of minor alternative energy transfer pathways. The ultimate confirmation of their role on the interchromophoric energy transfer can be achieved by performing nonadiabatic excited-state molecular dynamics simulations by selectively freezing the nuclear motions in question. Our results point out this strategy as a useful tool to identify and evaluate the impact of these vibrational funnels on the energy transfer processes and guide the in silico design of materials with tunable properties and enhanced functionalities. Our work encourages applications of this methodology to different chemical and biochemical processes such as reactive scattering and protein conformational changes, to name a few.

Pseudomonas aeruginosa and the Complement System: A Review of the Evasion Strategies.

The increasing emergence of multidrug resistant isolates of P. aeruginosa causes major problems in hospitals worldwide. This concern is particularly significant in bloodstream infections that progress rapidly, with a high number of deaths within the first hours and without time to select the most appropriate treatment. In fact, despite improvements in antimicrobial therapy and hospital care, P. aeruginosa bacteremia remains fatal in about 30% of cases. The complement system is a main defensive mechanism in blood against this pathogen. This system can mark bacteria for phagocytosis or directly lyse it via the insertion of a membrane attack complex in the bacterial membrane. P. aeruginosa exploits different strategies to resist complement attack. In this review for the special issue on "bacterial pathogens associated with bacteriemia", we present an overview of the interactions between P. aeruginosa and the complement components and strategies used by this pathogen to prevent recognition and killing by the complement system. A thorough understanding of these interactions will be critical in order to develop drugs to counteract bacterial evasion mechanisms.

Monitoring vibronic coherences and molecular aromaticity in photoexcited cyclooctatetraene with an X-ray probe: a simulation study.

Understanding conical intersection (CI) dynamics and subsequent conformational changes is key for exploring and controlling photo-reactions in aromatic molecules. Monitoring of their time-resolved dynamics remains a formidable experimental challenge. In this study, we simulate the photoinduced S3 to S1 non-adiabatic dynamics of cyclooctatetraene (COT), involving multiple CIs with relaxation times in good agreement with experiment. We further investigate the possibility to directly probe the CI passages in COT by off-resonant X-ray Raman spectroscopy (TRUECARS) and time-resolved X-ray diffraction (TRXD). We find that these signals sensitively monitor key chemical features during the ultrafast dynamics. First, we distinguish two CIs by using TRUECARS signals with their appearances at different Raman shifts. Second, we demonstrate that TRXD, where X-ray photons scatter off electron densities, can resolve ultrafast changes in the aromaticity of COT. It can further distinguish between planar and non-planar geometries explored during the dynamics, as e.g. two different tetraradical-type CIs. The knowledge gained from these measurements can give unique insight into fundamental chemical properties that dynamically change during non-adiabatic passages.

A Comparative Study of PMETAC-Modified Mesoporous Silica and Titania Thin Films for Molecular Transport Manipulation.

The manipulation and understanding of molecular transport across functionalized nanopores will take us closer to mimicking biological membranes and thus to design high-performance permselective separation systems. In this work, Surface-initiated atom transfer radical polymerization (SI-ATRP) of (2-methacryloyloxy)-ethyltrimethylammonium chloride (METAC) was performed on both mesoporous silica and mesoporous titania thin films. Pores were proven to be filled using ellipsometry and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). Furthermore, the employed method leads to a polymer overlayer, whose thickness could be discriminated using a double-layer ellipsometry model. Cyclic voltammetry experiments reveal that the transport of electrochemically active probes is affected by the PMETAC presence, both due to the polymer overlayer and the confined charge of the pore-tethered PMETAC. A more detailed study demonstrates that ion permeability depends on the combined role of the inorganic scaffolds' (titania and silica) surface chemistry and the steric and charge exclusion properties of the polyelectrolyte. Interestingly, highly charged negative walls with positively charged polymers may resemble zwitterionic polymer behavior in confined environments.

Improvement of the Antibacterial Activity of Phage Lysin-Derived Peptide P87 through Maximization of Physicochemical Properties and Assessment of Its Therapeutic Potential.

Phage lysins are a promising alternative to common antibiotic chemotherapy. However, they have been regarded as less effective against Gram-negative pathogens unless engineered, e.g., by fusing them to antimicrobial peptides (AMPs). AMPs themselves pose an alternative to antibiotics. In this work, AMP P87, previously derived from a phage lysin (Pae87) with a presumed nonenzymatic mode-of-action, was investigated to improve its antibacterial activity. Five modifications were designed to maximize the hydrophobic moment and net charge, producing the modified peptide P88, which was evaluated in terms of bactericidal activity, cytotoxicity, MICs or synergy with antibiotics. P88 had a better bactericidal performance than P87 (an average of 6.0 vs. 1.5 log-killing activity on Pseudomonas aeruginosa strains treated with 10 µM). This did not correlate with a dramatic increase in cytotoxicity as assayed on A549 cell cultures. P88 was active against a range of P. aeruginosa isolates, with no intrinsic resistance factors identified. Synergy with some antibiotics was observed in vitro, in complex media, and in a respiratory infection mouse model. Therefore, P88 can be a new addition to the therapeutic toolbox of alternative antimicrobials against Gram-negative pathogens as a sole therapeutic, a complement to antibiotics, or a part to engineer proteinaceous antimicrobials.

Exciton-vibrational dynamics induces efficient self-trapping in a substituted nanoring.

Cycloparaphenylenes, being the smallest segments of carbon nanotubes, have emerged as prototypes of the simplest carbon nanohoops. Their unique structure-dynamics-optical properties relationships have motivated a wide variety of synthesis of new related nanohoop species. Studies of how chemical changes, introduced in these new materials, lead to systems with new structural, dynamics and optical properties, expand their functionalities for optoelectronics applications. Herein, we study the effect that conjugation extension of a cycloparaphenylene through the introduction of a satellite tetraphenyl substitution has on its structural and dynamical properties. Our non-adiabatic excited state molecular dynamics simulations suggest that this substitution accelerates the electronic relaxation from the high-energy band to the lowest excited state. This is partially due to efficient conjugation achieved between specific phenyl units as introduced by the tetraphenyl substitution. We observe a particular exciton redistribution during relaxation, in which the tetraphenyl substitution plays a significant role. As a result, an efficient inter-band energy transfer takes place. Besides, the observed phonon-exciton interplay induces a significant exciton self-trapping. Our results encourage and guide the future studies of new phenyl substitutions in carbon nanorings with desired optoelectronic properties.

Effect of phytate on crystallization on ureteral stents and bacterial attachment: an in vitro study.

The use of double J ureteral stents can lead to several adverse effects, as urinary infection. Bacteria tend to colonize the stent surface, leading to the formation of bacterial biofilms. The presence of urease-producing bacteria increase the urine pH leading to the incrustation and blockage of the stent. On the other hand, these large crystalline masses function as niduses, allowing the attachment of even more bacteria and decreasing its exposure to antibiotics. The aim of this in vitro study was to assess the effect of phytate on the attachment of bacteria to the catheter surface under conditions that favor crystallization. Catheter sections were incubated in a synthetic urine medium (pH 6.5) in the presence or absence of Pseudomonas aeruginosa and phytate. Amount of calcium deposits was measured using an Arsenazo III colorimetric method and the number of attached bacteria to the stent was determined. Differences were assessed using an ANOVA with a Bonferroni post hoc test. The formation of calcium phosphate deposits (brushite and hydroxyapatite) and oxalate crystals (COM), as were as the amount of bacteria decreased when phytate was present. Thus, phytate successfully decreased bacterial adhesion by inhibiting the formation of crystalline deposits.

Infinitene: Computational Insights from Nonadiabatic Excited State Dynamics.

Progress in organic synthesis opens exploration of a rich diversity of molecules with interesting new structural topologies. This is the case of a recently synthesized helically twisted figure-eight molecule coined infinitene. The molecule belongs to a numerous family of looped polyarenes, where the degree of π-conjugation is controlled by high strain energies and steric hindrances. A particular balance of these ingredients leads to unusual optoelectronic properties potentially suitable for a range of applications in nanoelectronics and photonics. Due to its recent discovery, the photophysical properties of infinitene remain unexplored. In this Letter, atomistic nonadiabatic excited state molecular dynamics modeling unveils unique features of intramolecular electronic and vibrational energy relaxation and redistribution that take place after molecular photoexcitation. Our results detail relationships between optical and electronic properties providing useful knowledge for future molecular designs related to infinitene.

Charge-Transfer Luminescence in a Molecular Donor-Acceptor Complex: Computational Insights.

Donor-acceptor molecular complexes are a popular class of materials utilizing charge-transfer states for practical applications. A recent class of donor-acceptor dyads based on the fluorescent BODIPY functionalized with triphenylamine (TPA) shows the peculiar property of dual fluorescence. It is hypothesized that instead of the sensitized charge-transfer state being optically dark, it provides an additional bright radiative pathway. Here we use time-dependent density functional theory to characterize the energetic alignment of excitonic and charge-transfer states in a BODIPY-TPA molecular complex. We observe that using a long-range exchange corrected functional in combination with state-specific solvation scheme gives a qualitatively correct alignment of the exciton and charge-transfer states and an enhancement in oscillator strength for the equilibrium solvated charge-transfer state, in agreement with experiment. This work provides rationalization of charge-transfer state emission and provides a foundation to explore charge-transfer using ab initio excited-state nonadiabatic dynamics.

Adiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation.

We present a method to link the Nonadiabatic EXcited-state Molecular Dynamics (NEXMD) package to the SANDER package supplied by AMBERTOOLS to provide excited-state adiabatic quantum mechanics/molecular mechanics (QM/MM) simulations. NEXMD is a computational package particularly developed to perform simulations of the photoexcitation and subsequent nonadiabatic electronic and vibrational energy relaxation in large multichromophoric conjugated molecules involving several coupled electronic excited states. The NEXMD-SANDER exchange has been optimized in order to achieve excited-state adiabatic dynamics simulations of large conjugated materials in a QM/MM environment, such as an explicit solvent. Dynamics of a substituted polyphenylene vinylene oligomer (PPV3-NO2) in vacuum and different explicit solvents has been used as a test case by performing comparative analysis of changes in its optical spectrum, state-dependent conformational changes, and quantum bond orderings. The method has been tested and compared with respect to previous implicit solvent implementations. Also, the impact on the expansion of the QM region by including a variable number of solvent molecules has been analyzed. Altogether, these results encourage future implementations of NEXMD simulations using the same combination of methods.

Ultrafast coherent photoexcited dynamics in a trimeric dendrimer probed by X-ray stimulated-Raman signals.

The photoinduced ultrafast coherent inter-chromophore energy redistribution in a triarylamine trimer is explored using nonadiabatic excited state molecular dynamics followed by simulations of X-ray Raman signals. The nitrogencentered system ensures strong interchromophore interactions and, thus, the presence of coherences. Nevertheless, the multitude of non-deterministic photoinduced pathways during the ultrafast inter-branch migration of the excitation results in random confinement on some branches and, therefore, spatial exciton scrambling and loss of phase information at long times. We show that the vibronic coherence dynamics evolving into the incoherent scrambling mechanism on ultrafast 50 fs timescale, is accurately probed by the TRUECARS X-ray stimulated Raman signal. In combination with previous results, where the technique has revealed long-lived coherences in a rigid heterodimer, the signal is most valuable for detecting ultrafast molecular coherences or their absence. We demonstrate that X-ray Raman spectroscopy is a useful tool in the chemical design of functional molecular building blocks.