ABSTRACT
The efficiency of light-harvesting and energy transfer in multi-chromophore ensembles underpins natural photosynthesis. Dendrimers are highly branched synthetic multi-chromophoric conjugated supra-molecules that mimic these natural processes. After photoexcitation, their repeated units participate in a number of intramolecular electronic energy relaxation and redistribution pathways that ultimately funnel to a sink. Here, a model four-branched dendrimer with a pyrene core is theoretically studied using nonadiabatic molecular dynamics simulations. We evaluate excited-state photoinduced dynamics of the dendrimer, and demonstrate on-the-fly simulations of its transient absorption pump-probe (TA-PP) spectra. We show how the evolutions of the simulated TA-PP spectra monitor in real time photoinduced energy relaxation and redistribution, and provide a detailed microscopic picture of the relevant energy-transfer pathways. To the best of our knowledge, this is the first of this kind of on-the-fly atomistic simulation of TA-PP signals reported for a large molecular system.
ABSTRACT
Energy transfer processes among units of light-harvesting homo-oligomers impact the efficiency of these materials as components in organic optoelectronic devices such as solar cells. Perylene diimide (PDI), a prototypical dye, features exceptional light absorption and highly tunable optical and electronic properties. These properties can be modulated by varying the number of PDI units and linkers between them. Herein, atomistic nonadiabatic excited state molecular dynamics is used to explore the energy transfer during the internal conversion of acetylene and diacetylene bridged dimeric and trimeric PDIs. Our simulations reveal a significant impact of the bridge type on the transient exciton localization/delocalization between units of PDI dimers. After electronic relaxation, larger exciton delocalization occurs in the PDI dimer connected by the diacetylene bridge with respect to the one connected by the shorter acetylene bridge. These changes can be rationalized by the Frenkel exciton model. We outline a technique for deriving parameters for this model using inputs provided by nonadiabatic dynamics simulations. Frenkel exciton description reveals an interplay between the relative strengths of the diagonal and off-diagonal disorders. Moreover, atomistic simulations and the Frenkel exciton model of the PDI trimer systems corroborate in detail the localization properties of the exciton on the molecular units during the internal conversion to the lowest-energy excited state when the units become effectively decoupled. Overall, atomistic nonadiabatic simulations in combination with the Frenkel exciton model can serve as a predictive framework for analyzing and predicting desired exciton traps in PDI-based oligomers designed for organic electronics and photonic devices.
ABSTRACT
Pseudomonas aeruginosa is a common pathogen associated with recreational water facilities and poses risks to public health. However, data on the prevalence of P. aeruginosa in tourist destinations like the Canary Islands, Spain, remain limited. We assessed P. aeruginosa prevalence in 23 tourist facilities from 2016 to 2019. Compliance with water quality standards was evaluated, and 3962 samples were collected and analyzed. We examined different types of recreational water installations, including outer swimming pools, whirlpools, and cold wells. Of the sampled facilities, 31.2% did not comply with the current legislation's parametric values, mainly due to inadequate disinfectant levels, water temperature, and P. aeruginosa presence. The prevalence of P. aeruginosa was 4.8%, comparable to some European countries but lower than others. Cold wells displayed the highest non-compliance rate (89.2%) and yet exhibited a lower P. aeruginosa prevalence (1.9%) than outer swimming pools and whirlpools. Children's presence did not significantly impact P. aeruginosa contamination. Chlorine-based disinfectants are more effective than bromine-based ones in controlling P. aeruginosa. Regional variability in contamination was observed, with Fuerteventura showing lower colonization rates. Disinfectant levels play a critical role in P. aeruginosa control, and maintaining adequate levels is essential, particularly in bromine-treated installations. Our findings provide valuable insights into the prevalence and distribution of P. aeruginosa in recreational waters within tourist facilities. Tailored strategies are needed to ensure water safety in different Spanish regions. Continued monitoring and assessment, combined with artificial intelligence and machine learning, will enable the implementation of targeted interventions to protect the health of recreational water users.
ABSTRACT
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.
ABSTRACT
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.
Subject(s)
Blood Proteins , Complement Factor H , Pseudomonas aeruginosa , Humans , Complement Factor H/metabolism , Pseudomonas aeruginosa/metabolism , Opsonization , Protein Binding , Complement System Proteins/metabolism , Bacteria/metabolismABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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 fluorantheneâthe primary, commercially available anion reagentâinteracts 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 PTâalso described as HDXâmechanisms. 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.
Subject(s)
Protons , Tandem Mass Spectrometry , Deuterium , Carbohydrates , Anions , Deuterium Exchange Measurement/methodsABSTRACT
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.
ABSTRACT
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.
Subject(s)
Disinfectants , Pseudomonas aeruginosa , Humans , Spain/epidemiology , Water Microbiology , Water , Environmental MonitoringABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.
ABSTRACT
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.