Nuclear Quantum Effects in Proton or Hydrogen Transfer.

Proton or hydrogen transfers, basic chemical reactions, proceed either by thermally activated barrier crossing or via tunneling. Studies of molecules undergoing single or double proton or hydrogen transfer in the ground or excited electronic state reveal that tunneling can dominate under conditions usually considered to favor the thermal process. Moreover, the tunneling probability strongly varies for excitation of certain vibrational modes, which changes the effective barrier and/or proton transfer distance. When the reaction is fast compared to vibrational relaxation, the mode selectivity can still be maintained for molecules in solutions at 293 K. These observations point to dangers of relating the calculated minimum energy paths and the associated barriers to the experimentally obtained activation energies. The multidimensional character of the reaction coordinate is obvious; it can dramatically change for slowly and rapidly relaxing environments. We postulate that the hydrogen bond definition should be extended by specifically including the role of molecular vibrations.

Photodegradation of free base and zinc porphyrins in the presence and absence of oxygen.

Comparison of photostability in degassed and aerated toluene solutions is reported for 5,10,15,20-tetraphenylporphyrin, 5,10,15-tri(p-tolyl)porphyrin, and their zinc analogues. After degassing, quantum yields of photodegradation are higher, but the photodecomposition rates decrease. Lower stability in deoxygenated solutions is due to much longer triplet lifetimes: 200-300 microseconds, compared to 200-360 ns in non-degassed toluene. For the zinc porphyrins, the LC-MS results show that the initial photoproduct contains two oxygen atoms. Based on electronic absorption and calculations, it is assigned to dehydrated zinc biladienone structure, relatively stable in toluene, but readily demetallated in dichloromethane. A similar species is formed also in the case of free bases, but it then undergoes hydration due to traces of water present in the solvent. Zinc derivatives were found to form biladienones even in degassed solutions. To explain this observation, we postulate formation of a complex with remaining oxygen or oxygen-containing species which is not removed by freeze-thaw procedure. This hypothesis is confirmed by MS results and by the analysis of photodegradation products obtained when zinc porphyrin is complexed with dimethylsulfoxide (DMSO). Under these circumstances, changes in absorption are the same as in the absence of DMSO when non-degassed toluene is used, but irradiation of deoxygenated solutions leads to a different photoproduct. For both degassed and non-degassed solvents, complexation with DMSO results in the enhancement of photostability.

Anisotropic coupling of individual vibrational modes to a Cu(110) substrate.

We present a study on the excitation of individual vibrational modes with ballistic charge carriers propagating along the Cu(110) surface. By means of the molecular nanoprobe technique, where the reversible switching of a molecule-in this case tautomerization of porphycene-is utilized to detect excitation events, we reveal anisotropic coupling of two distinct vibrational modes to the substrate. The N-H bending mode, excited below |E| ≈ 376 meV, exhibits maxima perpendicular to the rows of the Cu(110) substrate and minima along the rows. In contrast, the N-H stretching mode, excited above |E| ≈ 376 meV, displays maxima along the rows and is constant otherwise. This inversion of the anisotropy reflects the orthogonality between the N-H bending and stretching mode. Additionally, we observe an energy-dependent asymmetry in the propagation direction of charge carriers injected into the Cu(110) surface state. Hereby, the anisotropic band structure results in a correlation between the group velocity and the tunneling probability into electronic states of the substrate.

SERS Signature of SARS-CoV-2 in Saliva and Nasopharyngeal Swabs: Towards Perspective COVID-19 Point-of-Care Diagnostics.

In this study, the intrinsic surface-enhanced Raman spectroscopy (SERS)-based approach coupled with chemometric analysis was adopted to establish the biochemical fingerprint of SARS-CoV-2 infected human fluids: saliva and nasopharyngeal swabs. The numerical methods, partial least squares discriminant analysis (PLS-DA) and support vector machine classification (SVMC), facilitated the spectroscopic identification of the viral-specific molecules, molecular changes, and distinct physiological signatures of pathetically altered fluids. Next, we developed the reliable classification model for fast identification and differentiation of negative CoV(-) and positive CoV(+) groups. The PLS-DA calibration model was described by a great statistical value-RMSEC and RMSECV below 0.3 and R2cal at the level of ~0.7 for both type of body fluids. The calculated diagnostic parameters for SVMC and PLS-DA at the stage of preparation of calibration model and classification of external samples simulating real diagnostic conditions evinced high accuracy, sensitivity, and specificity for saliva specimens. Here, we outlined the significant role of neopterin as the biomarker in the prediction of COVID-19 infection from nasopharyngeal swab. We also observed the increased content of nucleic acids of DNA/RNA and proteins such as ferritin as well as specific immunoglobulins. The developed SERS for SARS-CoV-2 approach allows: (i) fast, simple and non-invasive collection of analyzed specimens; (ii) fast response with the time of analysis below 15 min, and (iii) sensitive and reliable SERS-based screening of COVID-19 disease.

Solvent effects on the photooxidation of indolepyrazines.

Photodestruction of 2-(pyrazin-2'-yl)-1H-indole and 2,5-di(1H-indol-2'-yl)pyrazine involves singlet oxygen generation and its rapid insertion into the indole ring with the formation of benzoxazinone derivatives: 2-(pyrazin-2-yl)-4H-3,1-benzoxazin-4-one and 2-[5-(1H-indol-2-yl)pyrazin-2-yl]-4H-3,1-benzoxazin-4-one. The quantum yield of this reaction strongly depends on the environment. It is definitely smaller in protic methanol than in aprotic acetonitrile or n-hexane. The observed effect of photostabilization is explained by formation of hydrogen bonded complexes between the chromophore and alcohol, which results in lower triplet formation efficiency and, in consequence, decrease of singlet oxygen formation quantum yield.

Tautomerization of single asymmetric oxahemiporphycene molecules on Cu(111).

We have studied 22-oxahemiporphycene molecules by a combination of scanning tunneling microscopy at low temperatures and density functional theory calculations. In contrast to other molecular switches with typically two switching states, these molecules can in principle exist in three different tautomers, due to their asymmetry and three inequivalent binding positions of a hydrogen atom in their macrocycle. Different tautomers are identified from the typical appearance on the surface and tunneling electrons can be used to tautomerize single molecules in a controllable way with the highest rates if the STM tip is placed close to the hydrogen binding positions in the cavity. Characteristic switching processes are explained by the different energy pathways upon adsorption on the surface. Upon applying higher bias voltages, deprotonation occurs instead of tautomerization, which becomes evident in the molecular appearance.

Spectroscopic investigation of photophysics and tautomerism of amino- and nitroporphycenes.

Parent, unsubstituted porphycene and its two derivatives: 2,7,12,17-tetra-n-propylporphycene and 2,7,12,17-tetra-t-butylporphycene were substituted at the meso position with amino and nitro groups. These two families of porphycenes were characterized in detail with respect to their spectral, photophysical, and tautomeric properties. Two trans tautomers of similar energies coexist in the ground electronic state, but only one form dominates in the lowest excited singlet state. Absorption, magnetic circular dichroism (MCD), and emission anisotropy combined with quantum-chemical calculations led to the assignment of S1 and S2 transitions in both tautomers. Compared with the parent porphycene, the S1-S2 energy gap significantly increases; for one tautomeric form, the effect is twice as large as for the other. Both amino- and nitroporphycenes emit single fluorescence; previously reported dual emission of aminoporphycenes is attributed to a degradation product. Introduction of bulky t-butyl groups leads to a huge decrease in fluorescence intensity; this effect, arising from the interaction of the meso substituent with the adjacent t-butyl moiety, is particularly strong in the nitro derivative.

Isotope effects observed in diluted D2O/H2O mixtures identify HOD-induced low-density structures in D2O but not H2O.

Normal and heavy water are solvents most commonly used to study the isotope effect. The isotope effect of a solvent significantly influences the behavior of a single molecule in a solution, especially when there are interactions between the solvent and the solute. The influence of the isotope effect becomes more significant in D2O/H2O since the hydrogen bond in H2O is slightly weaker than its counterpart (deuterium bond) in D2O. Herein, we characterize the isotope effect in a mixture of normal and heavy water on the solvation of a HOD molecule. We show that the HOD molecule affects the proximal solvent molecules, and these disturbances are much more significant in heavy water than in normal water. Moreover, in D2O, we observe the formation of low-density structures indicative of an ordering of the solvent around the HOD molecule. The qualitative differences between HOD interaction with D2O and H2O were consistently confirmed with Raman spectroscopy and NMR diffusometry.

Solving the Puzzle of Unusual Excited-State Proton Transfer in 2,5-Bis(6-methyl-2-benzoxazolyl)phenol.

2,5-Bis(6-methyl-2-benzoxazolyl)phenol (BMP) exhibits an ultrafast excited-state intramolecular proton transfer (ESIPT) when isolated in supersonic jets, whereas in condensed phases the phototautomerization is orders of magnitude slower. This unusual situation leads to nontypical photophysical characteristics: dual fluorescence is observed for BMP in solution, whereas only a single emission, originating from the phototautomer, is detected for the ultracold isolated molecules. In order to understand the completely different behavior in the two regimes, detailed photophysical studies have been carried out. Kinetic and thermodynamic parameters of ESIPT were determined from stationary and transient picosecond absorption and emission for BMP in different solvents in a broad temperature range. These studies were combined with time-dependent- density functional theory quantum-chemical modeling. The excited-state double-well potential for BMP and its methyl-free analogue were calculated by applying different hybrid functionals and compared with the results obtained for another proton-transferring molecule, 2,5-bis(5-ethyl-2-benzoxazolyl)hydroquinone (DE-BBHQ). The results lead to the model that explains the difference in proton-transfer properties of BMP in vacuum and in the condensed phase by inversion of the two lowest singlet states occurring along the PT coordinate.

Influence of bulky substituents on single-molecule SERS sensitivity.

The surface-enhanced Raman spectroscopy (SERS) detection limit strongly depends on the molecular structure, which we demonstrate for a family of tert-butyl-substituted porphycenes. Even though the investigated species present very similar photophysical properties, the ratio between the SERS signal and fluorescence background depends on the number of bulky tert-butyl groups. Moreover, the probability of single molecule detection systematically drops with the number of the moieties attached to the pyrrole ring. As steric hindrance is the only significantly changing feature among the studied chromophores, we attribute the observed phenomena to the spatial structure. We also show that the sensitivity of the SERS technique can be improved by lowering the temperature. We managed to observe single-molecule spectra for derivatives for which this was unattainable at room temperature.

Scouting for strong light-matter coupling signatures in Raman spectra.

Strong coupling between vibrational transitions and a vacuum field of a cavity mode leads to the formation of vibrational polaritons. These hybrid light-matter states have been widely explored because of their potential to control chemical reactivity. However, the possibility of altering Raman scattering through the formation of vibrational polaritons has been rarely reported. Here, we present the Raman scattering properties of different molecules under vibrational strong coupling conditions. The polariton states are clearly observed in the IR transmission spectra of the coupled system for benzonitrile and methyl salicylate in liquid phase and for polyvinyl acetate in a solid polymer film. However, none of the studied systems exhibits a signature of the polariton states in the Raman spectra. For the solid polymer film, we have used cavities with different layer structures to investigate the influence of vibrational strong coupling on the Raman spectra. The only scenario where alterations of the Raman spectra are observed is for a thin Ag layer being in direct contact with the polymer film. This shows that, even though the system is in the vibrational strong coupling regime, changes in the Raman spectra do not necessarily result from the strong coupling, but are caused by the surface enhancement effects.

SERS-based sensor for the detection of sexually transmitted pathogens in the male swab specimens: A new approach for clinical diagnosis.

The surface-enhanced Raman scattering (SERS) has been widely tested for its usefulness in microbiological studies, providing many information-rich spectra which are a kind of 'whole-organism fingerprint' and enabling identification of bacterial species. Here we show, previously not considered, the comprehensive SERS-chemometric analysis of five bacterial pathogens, namely Neisseria gonorrhoeae, Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, and Haemophilus ducreyi, all being responsible for sexually transmitted diseases (STDs). In the designed biosensor, the direct, intrinsic format of the spectroscopic analysis was adopted for the SERS-based screening of gonorrhea and chlamydiosis due to vibrational analysis of men's urethra swabs. Our experiments demonstrated that the applied method enables identification the individual species of the Neisseria genus with high accuracy. In order to differentiate the sexually transmitted pathogens and to classify the clinical samples of male urethra swabs, three multivariate methods were used. In the external validation the created models correctly classified the men's urethra swabs with prediction accuracy reaching 89% for SIMCA and 100% for PLS-DA. As a result, the developed protocol enables: (i) simple and non-invasive analysis of clinical samples (the collection of urethra swabs specimens could be carried out at different points of care, such as doctor's office); (ii) fast analysis (<15 min); (iii) culture-free identification; (iv) sensitive and reliable SERS-based diagnosis of STD. The simplicity of the developed detection procedure, supported by high sensitivity, reproducibility, and specificity, open a new path in the improvement of the point-of-care applications.

Substituent screening effect on single-molecule photostability: comparison of three differently substituted porphycenes.

Photobleaching of single molecules has been studied using confocal fluorescence microscopy for porphycene, a porphyrin isomer, and its two derivatives. Fourfold substitution of porphycene with bulkytert-butyl groups leads to the enhancement of photostability, even though the spectral, photophysical, and redox parameters remain similar. We attribute this effect to the increase of the efficiency of physical quenching of the chromophore triplet state by oxygen, compared with the yield of chemical reaction that leads to photobleaching. Analysis of the observed photon fluxes from single emitters embedded in a polymer film shows that the experiment based on fluorescence is biased towards detection of molecules which have oxygen-the triplet quencher-in their vicinity. The distribution of the measured photodegradation quantum yields is very heterogeneous, suggesting that physical and chemical quenching rates exhibit different distance and orientation dependences.

Controlling Emissive Properties by Intramolecular Hydrogen Bonds: Alkyl and Aryl meso-Substituted Porphycenes.

Porphycene, a porphyrin isomer, is an efficient fluorophore. However, four-fold meso substitution with alkyl groups decreases the fluorescence quantum yield by orders of magnitude. For aryl substituents, this effect is small. To explain this difference, we have synthesized and studied a mixed aryl-alkyl-substituted compound, 9,20-diphenyl-10,19-dimethylporphycene, as well as the 9,20-diphenyl and 9,20-dimethyl derivatives. Analysis of the structural, spectroscopic, and photophysical data of the six porphycenes, combined with quantum chemical calculations, shows a clear correlation between the strength of the intramolecular NH⋅⋅⋅N hydrogen bonds and the efficiency of the radiationless depopulation of the lowest-excited singlet state. This result led us to propose a model in which the delocalization of the inner protons in the cavity of the macrocycle is responsible for the nonradiative deactivation channel. The applicability of the model is confirmed by the literature data for other alkyl- or aryl-substituted porphycenes. The finding of a correlation between structural and emissive characteristics enables a rational design of porphycenes with desired photophysical properties.

Photoinduced and ground state conversions in a cyclic ß-thioxoketone.

The photochemistry of a cyclic ß-thioxoketone (2-methyl-1-(2-thioxycyclohexyl)propan-1-one (MTPO)) is investigated by NMR, UV, and IR experiments supported by DFT calculations. MTPO exists as a tautomeric mixture of an enol and a thiol form. Irradiation at low temperature led to a cis-trans isomerization of the thiol form resulting in a rather unusual enethiol (3). This is followed by a transfer of the isopropyl methine proton onto the carbonyl carbon resulting in yet another enethiol isomer (4). The photoconversion mechanisms without water present are discussed. Photochemical experiments at ambient temperature showed involvement of water in the excited state and resulted in another keto-form (5). The same species was also obtained when the products of the low temperature experiments were kept in the dark at ambient temperature.

Fluorinated Porphycenes: Synthesis, Spectroscopy, Photophysics, and Tautomerism.

Six porphycenes have been synthesized, bearing one, two, or three fluorine atoms attached directly to the 18-π-electron system at the meso positions. These novel compounds have been characterized by structural, electrochemical, and spectral techniques, combined with quantum chemical calculations. In three fluoroporphycenes, the unsymmetric substitution pattern leads to the presence of two nonequivalent trans tautomeric forms. They have been identified using electronic absorption, emission, and magnetic circular dichroism spectroscopies. Their relative energies have been estimated for the ground and lowest excited electronic states. Tautomerization potential is quasi-symmetric in S0 , but becomes strongly nonsymmetric in S1 . Femtosecond transient absorption studies allowed determination of tautomerization rates, larger and similar for both directions of the double hydrogen transfer in S0 , lower and disparate in S1 . Fluoroporphycenes emerge as good candidates for detailed studies of mechanisms of double hydrogen transfer, as well as processes responsible for rapid radiationless excited state depopulation.

Spectrofluorometer: the excitation beam intensity calibration using a single standard solution.

The accurate, periodically updated excitation beam intensity correction is essential for conducting fluorescence spectroscopy research. This article describes a simple and inexpensive approach to reevaluate the excitation calibration curve of a spectrofluorometer using a single dye solution. The method shows excellent agreement with the data obtained using a certified calibration detector for the broad spectral range from 290 nm to 700 nm.

Influence of local microenvironment on the double hydrogen transfer in porphycene.

We performed time-resolved transient absorption and fluorescence anisotropy measurements in order to study tautomerization of porphycene in rigid polymer matrices at cryogenic temperatures. Studies were carried out in poly(methyl methacrylate) (PMMA), poly(vinyl butyral) (PVB), and poly(vinyl alcohol) (PVA). The results prove that in all studied media hydrogen tunnelling plays a significant role in the double hydrogen transfer which becomes very sensitive to properties of the environment below approx. 150 K. We also demonstrate that there exist two populations of porphycene molecules in rigid media: "hydrogen-transferring" molecules, in which tautomerization occurs on time scales below 1 ns and "frozen" molecules in which double hydrogen transfer is too slow to be monitored with nanosecond techniques. The number of "frozen" molecules increases when the sample is cooled. We explain this effect by interactions of guest molecules with a rigid host matrix which disturbs symmetry of porphycene and hinders tunnelling. Temperature dependence of the number of hydrogen-transferring molecules suggests that the factor which restores the symmetry of the double-minimum potential well in porphycene are intermolecular vibrations localized in separated regions of the amorphous polymer.

Towards More Photostable, Brighter, and Less Phototoxic Chromophores: Synthesis and Properties of Porphyrins Functionalized with Cyclooctatetraene.

Free base and zinc porphyrins functionalized with cyclooctatetraene (COT), a molecule known as a good triplet-state quencher, have been obtained and characterized in detail by structural, spectral, and photophysical techniques. Substitution with COT leads to a dramatic decrease of the intrinsic lifetime of the porphyrin triplet. As a result, photostability in oxygen-free solution increases by two to three orders of magnitude. In non-degassed solutions, improvement of photostability is about tenfold for zinc porphyrins, but the free bases become less photostable. Similar quantum yields of photodegradation in free base and zinc porphyrins containing the COT moiety indicate a common mechanism of photochemical decomposition. The new porphyrins are expected to be much less phototoxic, since the quantum yield of singlet oxygen formation strongly decreases because of the shorter triplet lifetime. The reduction of triplet lifetime should also enhance the brightness and reduce blinking in porphyrin chromophores emitting in single-molecule regime, since the duration of dark OFF states will be shorter.

Photoeradication of bacteria with porphycenes: Substituent effects on the efficiency.

Considering the world-wide problem of growing antibiotic resistance of bacteria, photodynamic inactivation (PDI) has a potential to become the treatment approach against some infectious diseases. In our study, four differently substituted porphycenes were compared in terms of their bactericidal activity against E. faecalis. All tested compounds had a similar photophysical characteristics, i.e., there were no significant differences in the location of absorption bands or molar absorption coefficients. Also, singlet oxygen generation quantum yields were very similar. Surprisingly, differently substituted porphycenes caused very diverse PDI effects. Special attention was drawn to the tert-butyl moieties. Our studies demonstrated that the presence of these substituents lowers the bactericidal potential significantly and can completely block the activity when more than one moiety is introduced to the molecule. The porphycenes lacking tert-butyl groups exhibited much higher PDI potential and we assign this effect to different interactions of the differently substituted porphycenes with the bacterial cells. Most likely, the presence of tert-butyls impairs cell penetration by the photosensitizer. These results remind that the favorable photophysical characteristics do not ensure that the compound considered as a potential PDI agent can reach the microbial cells.