Raman and infrared spectra and theoretical calculations of dipicolinic acid, dinicotinic acid, and their dianions

Single-cell analysis reveals microbial spore responses to sodium hypochlorite

Pollution from toxic spores has caused us a lot of problems because spores are extremely resistant and can survive most disinfectants. Therefore, the detection of spore response to disinfectant is of great significance for the development of effective decontamination strategies. In this work, we investigated the effect of 0.5% sodium hypochlorite on the molecular and morphological properties of single spores of Bacillus subtilis using single-cell techniques. Laser tweezers Raman spectroscopy showed that sodium hypochlorite resulted in Ca2+-dipicolinic acid release and nucleic acid denaturation. Atomic force microscopy showed that the surface of treated spores changed from rough to smooth, protein shells were degraded at 10 min, and the permeability barrier was destroyed at 15 min. The spore volume decreased gradually over time. Live-cell imaging showed that the germination and growth rates decreased with increasing treatment time. These results provide new insight into the response of spores to sodium hypochlorite.

Ga(III) pyridinecarboxylate complexes: potential analogues of the second generation of therapeutic Ga(III) complexes?

A series of novel Ga(III)-pyridine carboxylates ([Ga(Pic)3]·H2O (GaPic; HPic = picolinic acid), H3O[Ga(Dpic)2]·H2O (GaDpic; H2Dpic = dipicolinic acid), [Ga(Chel)(H2O)(OH)]2·4H2O (GaChel; H2Chel = chelidamic acid) and [Ga(Cldpic)(H2O)(OH)]2 (GaCldpic; H2Cldpic = 4-chlorodipicolinic acid)) have been synthesized by simple one-step procedure. Vibrational spectroscopy (mid-IR), elemental analysis, thermogravimetric analysis and X-ray diffraction confirmed complexes molecular structure, inter and intramolecular interactions and their influence to spectral and thermal properties. Moreover, complex species speciation was described in Ga(III)-HPic and Ga(III)-H2Dpic systems by potentiometry and 1H NMR spectroscopy and mononuclear complex species were determined; [Ga(Pic)2]+ (logβ021 = 16.23(6)), [Ga(Pic)3] (logβ031 = 20.86(2)), [Ga(Dpic)2]- (logβ021 = 15.42(9)) and [Ga(Dpic)2(OH)]2- (logβ-121 = 11.08(4)). To confirm the complexes stability in 1% DMSO (primary solvent for biological testing), timescale 1H NMR spectra were measured (immediately after dissolution up to 96 h). Antimicrobial activity evaluated by IC50 (0.05 mM) is significant for GaDpic and GaCldpic against difficult to treat and multi-resistant P. aeruginosa. On the other hand, the GaPic complex is most effective against Jurkat, MDA-MB-231 and A2058 cancer cell lines and significantly also decreases the HepG2 cancer cells viability at 75 and 100 μM concentrations in a relatively short time (up to 48 h). In addition, fluorescence measurements have been used to elucidate bovine serum albumin binding activity between ligands, Ga(III) complexes and bovine serum albumin.

Physico-chemical characterization of single bacteria and spores using optical tweezers

Spore-forming pathogenic bacteria are adapted for adhering to surfaces, and their endospores can tolerate strong chemicals making decontamination difficult. Understanding the physico-chemical properties of bacteria and spores is therefore essential in developing antiadhesive surfaces and disinfection techniques. However, measuring physico-chemical properties in bulk does not show the heterogeneity between cells. Characterizing bacteria on a single-cell level can thereby provide mechanistic clues usually hidden in bulk measurements. This paper shows how optical tweezers can be applied to characterize single bacteria and spores, and how physico-chemical properties related to adhesion, fluid dynamics, biochemistry, and metabolic activity can be assessed.

Label-Free Identification of Spore-Forming Bacteria Using Ultrabroadband Multiplex Coherent Anti-Stokes Raman Scattering Microspectroscopy

Spore-forming bacteria accumulate dipicolinic acid (DPA) to form spores to survive in extreme environments. Vibrational spectroscopy is widely used to detect DPA and elucidate the existence of the bacteria, while vegetative cells, another form of spore-forming bacteria, have not been studied extensively. Herein, we applied coherent anti-Stokes Raman scattering (CARS) microscopy to spectroscopically identify both spores and vegetative cells without staining or molecular tagging. The spores were identified by the strong CARS signals due to DPA. Furthermore, we observed bright spots in the vegetative cells in the CARS image at 1735 cm^-1. The vegetative cells contained molecular species with C=O bonds because this vibrational mode was associated with the carbonyl group. One of the candidate molecular species is diketopimelic acid (DKP), a DPA precursor. This hypothesis was verified by comparing the spectrum obtained by the vegetative cells with that of the DKP analogue (ketopimelic acid) and with the result obtained by DFT calculation. The results indicate that the observed vegetative cell is in the sporulation process. CARS spectra can be used to monitor the maturation and preformation of spores.

Hypervirulent R20291 Clostridioides difficile spores show disinfection resilience to sodium hypochlorite despite structural changes

BACKGROUND

Clostridioides difficile is a spore forming bacterial species and the major causative agent of nosocomial gastrointestinal infections. C. difficile spores are highly resilient to disinfection methods and to prevent infection, common cleaning protocols use sodium hypochlorite solutions to decontaminate hospital surfaces and equipment. However, there is a balance between minimising the use of harmful chemicals to the environment and patients as well as the need to eliminate spores, which can have varying resistance properties between strains. In this work, we employ TEM imaging and Raman spectroscopy to analyse changes in spore physiology in response to sodium hypochlorite. We characterize different C. difficile clinical isolates and assess the chemical's impact on spores' biochemical composition. Changes in the biochemical composition can, in turn, change spores' vibrational spectroscopic fingerprints, which can impact the possibility of detecting spores in a hospital using Raman based methods.

RESULTS

We found that the isolates show significantly different susceptibility to hypochlorite, with the R20291 strain, in particular, showing less than 1 log reduction in viability for a 0.5% hypochlorite treatment, far below typically reported values for C. difficile. While TEM and Raman spectra analysis of hypochlorite-treated spores revealed that some hypochlorite-exposed spores remained intact and not distinguishable from controls, most spores showed structural changes. These changes were prominent in B. thuringiensis spores than C. difficile spores.

CONCLUSION

This study highlights the ability of certain C. difficile spores to survive practical disinfection exposure and the related changes in spore Raman spectra that can be seen after exposure. These findings are important to consider when designing practical disinfection protocols and vibrational-based detection methods to avoid a false-positive response when screening decontaminated areas.

pH-induced changes in Raman, UV-vis absorbance, and fluorescence spectra of dipicolinic acid (DPA)

Dipicolinic acid (DPA) is an essential component for the protection of DNA in bacterial endospores and is often used as a biomarker for spore detection. Depending upon the pH of the solution, DPA exists in different ionic forms. Therefore, it is important to understand how these ionic forms influence spectroscopic response. In this work, we characterize Raman and absorption spectra of DPA in a pH range of 2.0-10.5. We show that the ring breathing mode Raman peak of DPA shifts from 1003 cm^-1 to 1017 cm^-1 and then to 1000 cm^-1 as pH increases from 2 to 5. The relative peak intensities related to the different ionic forms of DPA are used to experimentally derive the pK_a values (2.3 and 4.8). We observe using UV-vis spectroscopy that the changes in the absorption spectrum of DPA as a function of pH correlate with the changes observed in Raman spectroscopy, and the same pK_a values are verified. Lastly, using fluorescence spectroscopy and exciting a DPA solution at between 210-330 nm, we observe a shift in fluorescence emission from 375 nm to 425 nm between pH 2 and pH 6 when exciting at 320 nm. Our work shows that the different spectral responses from the three ionic forms of DPA may have to be taken into account in, e.g., spectral analysis and for detection applications.

Photoacoustic remote sensing of suspicious objects for defence and forensic applications

Quantum cascade laser (QCL) based photoacoustic spectroscopic technique has been developed for detection of hazardous molecules contaminants/adsorbed on surfaces such as plastic and cloth from short standoff distances. The laser source and detection system is integrated together in a single unit. Spectra were recorded for traces of various molecules in mid-infrared spectral band (1130-1430 cm^-1) from distance of 0.5 m. Pulsed quantum cascade laser source, modulated at 25 kHz and 42 kHz frequency was used to detect molecular species adsorbed on surfaces of cloth and plastic. Ultrasonic microphones operating at 25 and 42 kHz resonant frequencies were used as detectors. The photoacoustic spectra of hazardous chemicals, explosive materials and bio-chemicals such as acetic acid, PETN (pentaerythritol tetranitrate), DPA (dipicolinic acid) in very low quantities were recorded. Sensitivities of 5 and 10 μg/cm² of these analytes were achieved with frequencies of 25 and 42 kHz respectively at distance of 0.5 m. In the present technique there was no interference of audio frequency (20 Hz to 20 kHz) and bright sunlight. The technique can be applied for screening of suspicious objects for homeland security and forensic applications. The present spectroscopic technique can be developed in man portable standalone product.

Crystallographic structure and crystal field parameters in the [AnIV(DPA)3]2− series, An = Th, U, Np, Pu

The [An^IV(DPA)₃]²⁻ series with An = Th, U, Np, Pu has been synthesized and characterized using SC-XRD, vibrational spectroscopy, and first principles calculations.

Endophytic Paenibacillus amylolyticus KMCLE06 Extracted Dipicolinic Acid as Antibacterial Agent Derived via Dipicolinic Acid Synthetase Gene

Bioactive natural compounds play pivotal roles in drug discovery and the emergence of multi-drug resistance pathogens demands the development of better/new drugs. Paenibacillus amylolyticus KMCLE06 endophytic bacterium isolated from the medicinal plant Coix lachryma-jobi were analyzed for the potential bioactive secondary metabolite compounds and its gene responsible within polyketide synthases (PKS) clusters. Ethyl acetate extraction of P. amylolyticus KMCLE06 showed significant antibacterial activity which was further processed to partial purification and characterization for bioactive compound. The foremost bioactive component in extraction was found to be dipicolinic acid (DPA). The antibacterial activity showed remarkable activity compared to the commercial standard DPA against both gram-positive and gram-negative pathogens. The MIC and MBC concentrations for partially purified extracted DPA ranged from 62.5 to 125 µg/ml and MBC from 208 to 250 µg/ml, respectively. Sequence analysis of gene amplified using degenerative primer, amplified 543 bp DNA region, revealing conserved putative open reading frame for dipicolinic acid synthetase (DpsA) key gene to produce DPA in most endospore forming bacteria. A search in the structural database for DpsA revealed significant homologous match with enoyl reductase one of the PKS type 1 module protein. This emphasizes endophytic P. amylolyticus KMCLE06 bacteria has presence of spoVF operon producing DPA via dipicolinic acid synthetase and lacks the polyketide synthase type 1 module cluster gene in its genome. And the bioactive compound DPA extracted acts as a stable remarkable antibacterial agent which can be potent compound for multi-resistance pathogens.

Molecular structure investigation of neutral, dimer and anion forms of 3,4-pyridinedicarboxylic acid: a combined experimental and theoretical study

In this study, the structural and vibrational analysis of 3,4-pyridinedicarboxylic acid (3,4-PDCA) are presented using experimental techniques as FT-IR, FT-Raman, NMR, UV and quantum chemical calculations. FT-IR and FT-Raman spectra of 3,4-pyridinedicarboxylic acid in the solid phase are recorded in the region 4000-400 cm(-1) and 4000-50 cm(-1), respectively. The geometrical parameters and energies of all different and possible monomer, dimer, anion(-1) and anion(-2) conformers of 3,4-PDCA are obtained from Density Functional Theory (DFT) with B3LYP/6-311++G(d,p) basis set. There are sixteen conformers (C1C16) for this molecule (neutral form). The most stable conformer of 3,4-PDCA is the C1 conformer. The complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes calculated with scaled quantum mechanics (SQM) method. (1)H and (13)C NMR spectra are recorded and the chemical shifts are calculated by using DFT/B3LYP methods with 6-311++G(d,p) basis set. The UV absorption spectrum of the studied compound is recorded in the range of 200-400 nm by dissolved in ethanol. The optimized geometric parameters were compared with experimental data via the X-ray results derived from complexes of this molecule. In addition these, molecular electrostatic potential (MEP), thermodynamic and electronic properties, HOMO-LUMO energies and Mulliken atomic charges, are performed.

Organosilatranes with thioester-anchored heterocyclic ring assembly: Cu2+ ion binding and fabrication of hybrid silica nanoparticles

Thioester allied organosilatranes were synthesized by the CDI mediated coupling of carboxylic acids with mercaptopropylsilatrane. One of the silatrane was further immobilized onto silica nanospheres, characterized and tested for copper ion binding.

Spectroscopy and viability of Bacillus subtilis spores after ultraviolet irradiation: implications for the detection of potential bacterial life on Europa

One of the most habitable environments in the Solar System outside of Earth may exist underneath the ice on Europa. In the near future, our best chance to look for chemical signatures of a habitable environment (or life itself) will likely be at the inhospitable icy surface. Therefore, it is important to understand the ability of organic signatures of life and life itself to persist under simulated europan surface conditions. Toward that end, this work examined the UV photolysis of Bacillus subtilis spores and their chemical marker dipicolinic acid (DPA) at temperatures and pressures relevant to Europa. In addition, inactivation curves for the spores at 100 K, 100 K covered in one micron of ice, and 298 K were measured to determine the probability for spore survival at the surface. Fourier transform infrared spectra of irradiated DPA showed a loss of carboxyl groups to CO2 as expected but unexpectedly showed significant opening of the heterocyclic ring, even for wavelengths>200 nm. Both DPA and B. subtilis spores showed identical unknown spectral bands of photoproducts after irradiation, further highlighting the importance of DPA in the photochemistry of spores. Spore survival was enhanced at 100 K by ∼5× relative to 298 K, but 99.9% of spores were still inactivated after the equivalent of ∼25 h of exposure on the europan surface.

Determination of structural and vibrational spectroscopic features of neutral and anion forms of dinicotinic acid by using NMR, infrared and Raman experimental methods combined with DFT and HF

In this study; the experimental (NMR, infrared and Raman) and theoretical (HF and DFT) analysis of dinicotinic acid were presented. (1)H and (13)C NMR spectra were recorded in DMSO solution and chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The vibrational spectra of dinicotinic acid were recorded by FT-Raman and FT-IR spectra in the range of 4000-10 cm(-1) and 4000-400 cm(-1), respectively. To determine the most stable neutral conformer of molecule, the selected torsion angle was changed every 10° and molecular energy profile was calculated from 0° to 360°. The geometrical parameters and energies were obtained for all conformers form from density functional theory (DFT/B3LYP) and HF with 6-311++G(d,p) basis set calculations. However, the results of the most stable neutral and two anion forms (anion(-1) and anion(-2) forms) of dinicotinic acid are reported here. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational wavenumbers, calculated with scaled quantum mechanics (SQM) method and PQS program.

Direct analysis of water content and movement in single dormant bacterial spores using confocal Raman microspectroscopy and Raman imaging

Heavy water (D2O) has a distinct molecular vibration spectrum, and this has been used to analyze the water content, distribution, and movement in single dormant Bacillus cereus spores using confocal Raman microspectroscopy and Raman imaging. These methods have been used to measure the kinetics of D2O release from spores suspended in H2O, the spatial distribution of D2O in spores, and the kinetics of D2O release from spores during dehydration in air at room temperature. The results obtained were as follows. (1) The Raman spectrum of single D2O-loaded dormant spores suggests that D2O in spores is in a relatively weak hydrogen-bonded mode, compared to the strong hydrogen-bonded mode in pure D2O. (2) The D2O content of individual spores in a population was somewhat heterogeneous. (3) The spatial distribution of D2O in single dormant spores is uneven, and is less dense in the central core region. Raman images of different molecular components indicate that the water distribution is somewhat different from those of proteins and Ca-dipicolinic acid. (4) Exchange of spore D2O with external H2O took place in less than 1 s. (5) However, release of spore D2O during air dehydration at room temperature was slow and heterogeneous and took 2-3 h for complete D2O release.

Screen-printed fluorescent sensors for rapid and sensitive anthrax biomarker detection

Since the 2001 anthrax attacks, efforts have focused on the development of an anthrax detector with rapid response and high selectivity and sensitivity. Here, we demonstrate a fluorescence sensor for detecting anthrax biomarker with high sensitivity and selectivity using a screen-printing method. A lanthanide-ethylenediamine tetraacetic acid complex was printed on a flexible polyethersulfone film. Screen-printing deposition of fluorescent detecting moieties produced fluorescent patterns that acted as a visual alarm against anthrax.

Spectroscopic characterization, X-ray structure, antimicrobial activity and DFT calculations of novel dipicolinate copper(II) complex with 2,6-pyridinedimethanol

Novel dipicolinate complex of copper(II) ion, [Cu(dmp)(dpc)]·0.8H(2)O [dmp: 2,6-pyridinedimethanol; dpc: dipicolinate or pyridine-2,6-dicarboxylate], has been prepared and fully characterized by single crystal X-ray structure determination. The central copper(II) ion is bonded to dpc and dmp ligands through pyridine nitrogen atom together with two oxygen atom, forming the distorted octahedral geometry. The complex molecules, connected via O-H···O hydrogen bonds, form a supramolecular structure. H(2)dpc, [Cu(dpc)(H(2)O)(3)] and [Cu(dmp)(dpc)]·0.8H(2)O were screened for antimicrobial activity against Gram-positive, Gram-negative bacteria and yeast. H(2)dpc and [Cu(dpc)(H(2)O)(3)] exhibited antibacterial and antifungal activity, while [Cu(dmp)(dpc)]·0.8H(2)O exhibited activity only for Gram-positive bacteria. The geometry optimization and EPR parameters were carried out using the following unrestricted hybrid density functionals: LSDA, BPV86, B3LYP, B3PW91, MPW1PW91, PBEPBE and HCTH. Although the supramolecular interactions have some influences on the molecular geometry in solid state phase, calculated data show that the predicted geometries can reproduce the structural parameters. The electronic station in the frontier orbitals of the copper complex calculated from the experimental data is compared to the results of time-depended DFT calculations with the polarizable continuum model. Calculated vibrational frequencies are consistent with the experimental IR data.