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1.
Spectrochim Acta A Mol Biomol Spectrosc ; 285: 121909, 2023 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-36170776

RESUMO

For effective treatment, it is crucial to identify the infecting bacterium at the species level and to determine its antimicrobial susceptibility. This is especially true now, when numerous bacteria have developed multidrug resistance to most commonly used antibiotics. Currently used methods need âˆ¼ 48 h to identify a bacterium and determine its susceptibility to specific antibiotics. This study reports the potential of using infrared spectroscopy with machine learning algorithms to identify E. coli isolated directly from patients' urine while simultaneously determining its susceptibility to antibiotics within âˆ¼ 40 min after receiving the patient's urine sample. For this goal, 1,765 E. coli isolates purified directly from urine samples were collected from patients with urinary tract infections (UTIs). After collection, the samples were tested by infrared microscopy and analyzed by machine learning. We achieved success rates of âˆ¼ 96% in isolate level identification and âˆ¼ 84% in susceptibility determination.


Assuntos
Infecções por Escherichia coli , Escherichia coli , Humanos , Testes de Sensibilidade Microbiana , Antibacterianos/farmacologia , Espectrofotometria Infravermelho , Aprendizado de Máquina , Infecções por Escherichia coli/tratamento farmacológico , Infecções por Escherichia coli/microbiologia
2.
Sci Total Environ ; 856(Pt 1): 159060, 2023 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-36174702

RESUMO

Microplastics are ubiquitous in the environment, including in food and drinking water. Consequently, there is growing concern about the human health risks associated with microplastic exposure through diet. However, the occurrence of microplastics in the human body, particularly in mothers and fetuses, is incompletely understood because of the limited amount of data on their presence in the body and the human placenta. This study evaluated the presence and characteristics of microplastics in 17 placentas using laser direct infrared (LD-IR) spectroscopy. Microplastics were detected in all placenta samples, with an average abundance of 2.70 ± 2.65 particles/g and a range of 0.28 to 9.55 particles/g. Among these microplastics, 11 polymer types were identified. The microplastics were mainly composed of polyvinyl chloride (PVC, 43.27 %), polypropylene (PP, 14.55 %), and polybutylene succinate (PBS, 10.90 %). The sizes of these microplastics ranged from 20.34 to 307.29 µm, and most (80.29 %) were smaller than 100 µm. Most of the smaller microplastics were fragments, but fibers dominated the larger microplastics (200-307.29 µm). Interestingly, the majority of PVC and PP were smaller than 200 µm. This study provides a clearer understanding of the shape, size, and nature of microplastics in the human placenta. Importantly, these data also provide crucial information for performing risk assessments of the exposure of fetuses to microplastics in the future.


Assuntos
Microplásticos , Poluentes Químicos da Água , Humanos , Feminino , Gravidez , Plásticos , Cloreto de Polivinila , Monitoramento Ambiental , Poluentes Químicos da Água/análise , Espectrofotometria Infravermelho , Lasers , Placenta/química
3.
Anal Chem ; 94(45): 15564-15569, 2022 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-36321942

RESUMO

Photothermal induced resonance (PTIR), an atomic force microscopy (AFM) analogue of IR spectroscopy also known as AFM-IR, is capable of nanoscale lateral resolution and finds broad applications in biology and materials science. Here, the spectral range of a top-illumination PTIR setup operating in contact-mode is expanded for the first time to the visible and near-IR spectral ranges. The result is a tool that yields absorption spectra and maps of electronic and vibrational features with spatial resolution down to ≈10 nm. In addition to the improved resolution, the setup enables light-polarization-dependent PTIR experiments in the visible and near-IR ranges for the first time. While previous PTIR implementations in the visible used total internal reflection illumination requiring challenging sample preparations on an optically transparent prism, the top illumination used here greatly simplifies sample preparation and will foster a broad application of this method.


Assuntos
Iluminação , Espectrofotometria Infravermelho/métodos , Microscopia de Força Atômica/métodos
4.
Sci Rep ; 12(1): 18972, 2022 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-36348038

RESUMO

Significant efforts have been done in last two decades to develop nanoscale spectroscopy techniques owning to their great potential for single-molecule structural detection and in addition, to resolve open questions in heterogeneous biological systems, such as protein-DNA complexes. Applying IR-AFM technique has become a powerful leverage for obtaining simultaneous absorption spectra with a nanoscale spatial resolution for studied proteins, however the AFM-IR investigation of DNA molecules on surface, as a benchmark for a nucleoprotein complexes nanocharacterization, has remained elusive. Herein, we demonstrate methodological approach for acquisition of AFM-IR mapping modalities with corresponding absorption spectra based on two different DNA deposition protocols on spermidine and Ni2+ pretreated mica surface. The nanoscale IR absorbance of distinctly formed DNA morphologies on mica are demonstrated through series of AFM-IR absorption maps with corresponding IR spectrum. Our results thus demonstrate the sensitivity of AFM-IR nanospectroscopy for a nucleic acid research with an open potential to be employed in further investigation of nucleoprotein complexes.


Assuntos
Silicatos de Alumínio , DNA , Microscopia de Força Atômica/métodos , Silicatos de Alumínio/química , Nucleoproteínas , Espectrofotometria Infravermelho/métodos
5.
Proc Natl Acad Sci U S A ; 119(47): e2210516119, 2022 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-36375054

RESUMO

Nearfield spectroscopic imaging techniques can be a powerful tool to map both cellular ultrastructure and molecular composition simultaneously but are currently limited in measurement capability. Resonance enhanced (RE) atomic force microscopy infrared (AFM-IR) spectroscopic imaging offers high-sensitivity measurements, for example, but probe-sample mechanical coupling, nonmolecular optical gradient forces, and noise overwhelm recorded chemical signals. Here, we analyze the key factors limiting AFM-IR measurements and propose an instrument design that enables high-sensitivity nanoscale IR imaging by combining null-deflection measurements with RE sensitivity. Our developed null-deflection scanning probe IR (NDIR) spectroscopic imaging provides ∼24× improvement in signal-to-noise ratio (SNR) compared with the state of the art, enables optimal signal recording by combining cantilever resonance with maximum laser power, and reduces background nonmolecular signals for improved analytical accuracy. We demonstrate the use of these properties for high-sensitivity, hyperspectral imaging of chemical domains in 100-nm-thick sections of cellular acini of a prototypical cancer model cell line, MCF-10A. NDIR chemical imaging enables facile recording of label-free, chemically accurate, high-SNR vibrational spectroscopic data from nanoscale domains, paving the path for routine studies of biomedical, forensic, and materials samples.


Assuntos
Lasers , Espectrofotometria Infravermelho/métodos , Microscopia de Força Atômica/métodos , Linhagem Celular
6.
Int J Mol Sci ; 23(21)2022 Oct 31.
Artigo em Inglês | MEDLINE | ID: mdl-36362033

RESUMO

The spectral range of femtosecond time-resolved infrared spectroscopy is limited by the bandwidth of mid-IR pulses (100~400 cm-1) generated from the combination of Ti:Sapphire amplifier, Optical Parametric Amplifier (OPA), and Difference Frequency Generation (DFG). To overcome this limitation, we implement a compact continuum mid-IR source producing ultrafast pulses that span the frequency range from 1000 to 4200 cm-1 (from 10 to 2.4 µm), which utilize the mixing of fundamental, second-harmonic, and third-harmonic of 800 nm pulse in the air. After building an IR spectrometer with continuum IR and a monochromator, we found that the distortion of the measured IR spectrum originated from the contamination of higher-order diffraction. We used bandpass filters to eliminate the higher-order contributions and correct the measured IR spectrum. We further characterized the spectral properties of fundamental, second-harmonic, and third-harmonic fields after the plasmonic filamentation process, which helps to improve the efficiency of the continuum IR generation. Using the generated continuum IR pulses, we measured the IR absorption spectrum of a water-benzonitrile mixture, which was found to be consistent with the spectrum obtained with a commercial FT-IR spectrometer. The present work will be useful for the efficient generation of continuum IR pulses for IR pump-probe and two-dimensional IR spectroscopy experiments in the future.


Assuntos
Água , Espectroscopia de Infravermelho com Transformada de Fourier , Espectrofotometria Infravermelho/métodos
7.
J Phys Chem B ; 126(45): 9246-9260, 2022 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-36326184

RESUMO

Despite its success as an anticancer drug, cisplatin suffers from resistance and produces side effects. To overcome these limitations, amino-acid-linked cisplatin analogues have been investigated. Lysine-linked cisplatin, Lysplatin, (Lys)PtCl2, exhibited outstanding reactivity toward DNA and RNA that differs from that of cisplatin. To gain insight into its differing reactivity, the structure of Lysplatin is examined here using infrared multiple photon dissociation (IRMPD) action spectroscopy. To probe the influence of the local chemical environment on structure, the deprotonated and sodium-cationized Lysplatin complexes are examined. Electronic structure calculations are performed to explore possible modes of binding of Lys to Pt, their relative stabilities, and to predict their infrared spectra. Comparisons of the measured IRMPD and predicted IR spectra elucidate the structures contributing to the experimental spectra. Coexistence of two modes of binding of Lys to Pt is found where Lys binds via the backbone and side-chain amino nitrogen atoms, NNs, or to the backbone amino and carboxylate oxygen atoms, NO-. Glycine-linked cisplatin and arginine-linked cisplatin complexes have previously been found to bind only via the NO- binding mode. Present results suggest that the NNs binding conformers may be key to the outstanding reactivity of Lysplatin toward DNA and RNA.


Assuntos
Lisina , Platina , Lisina/química , Cisplatino , Espectrofotometria Infravermelho/métodos , RNA
8.
J Phys Chem Lett ; 13(45): 10522-10526, 2022 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-36342244

RESUMO

Spontaneous aggregation of amyloid beta (Aß) proteins leading to the formation of oligomers and eventually into fibrils has been identified as a key pathological signature of Alzheimer's disease. The structure of late-stage aggregates have been studied in depth by conventional structural biology techniques, including nuclear magnetic resonance, X-ray crystallography, and infrared spectroscopy; however, the structure of early-stage aggregates is less known due to their transient nature. As a result, the structural evolution of amyloid aggregates from early oligomers to mature fibrils is still not fully understood. Here, we have applied atomic force microscopy-infrared nanospectroscopy to investigate the aggregation of Aß 16-22, which spans the amyloidogenic core of the Aß peptide. Our results demonstrate that Aß 16-22 involves a structural transition from oligomers with parallel ß-sheets to antiparallel fibrils through disordered and possibly helical intermediate fibril structures, contrary to the known aggregation pathway of full-length Aß.


Assuntos
Doença de Alzheimer , Peptídeos beta-Amiloides , Humanos , Peptídeos beta-Amiloides/química , Conformação Proteica em Folha beta , Amiloide/química , Doença de Alzheimer/metabolismo , Espectrofotometria Infravermelho , Fragmentos de Peptídeos/química
9.
Anal Chem ; 94(46): 16050-16059, 2022 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-36346912

RESUMO

Dimensional reduction of highly multidimensional datasets such as those acquired by Fourier transform infrared spectroscopy (FTIR) is a critical step in the data analysis workflow. To achieve this goal, numerous feature selection methods have been developed and applied in a supervised context, i.e., using a priori knowledge about data usually in the form of labels for classification or quantitative values for regression. For this, genetic algorithms have been largely exploited due to their flexibility and global optimization principle. However, few applications in an unsupervised context have been reported in infrared spectroscopy. The aim of this article is to propose a new unsupervised feature selection method based on a genetic algorithm using a validity index computed from KMeans partitions as a fitness function. Evaluated on a simulated dataset and validated and tested on three real-world infrared spectroscopic datasets, our developed algorithm is able to find the spectral descriptors improving clustering accuracy and simplifying the spectral interpretation of results.


Assuntos
Algoritmos , Análise por Conglomerados , Espectroscopia de Infravermelho com Transformada de Fourier , Espectrofotometria Infravermelho
10.
Phys Chem Chem Phys ; 24(43): 26890-26897, 2022 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-36317665

RESUMO

We report fingerprint infrared multiple-photon dissociation (IRMPD) spectra of the isolated gaseous hexa-coordinated complex of the macrocycle hexa-aza-18-crown-6 (hexacyclen, 1,4,7,10,13,16-hexaazacyclooctadecane, 18-azacrown-6) with Ni2+. The metal-ligand complexes are generated using electrospray ionization (ESI) and IR action spectra are recorded in a Fourier transform ion cyclotron resonance mass spectrometer (FTICR) MS coupled to the infrared free-electron laser FELIX. We investigate geometric structure of the complexes and in particular the chelation motif, by comparison with computed vibrational spectra, obtained using density functional theory (DFT) at the B3LYP/6-31++G(d,p) level. The quasi-octahedral chelation motif of the complex has been well documented in condensed-phase studies, and we focus here on the gas-phase structure, addressing in particular the question of a facial (fac) versus a meridional (mer) octahedral chelation geometry. Based on the good agreement between calculated linear IR spectra and experimental IRMPD spectra, we conclude that the gas-phase complex adopts a mer chelation geometry and we exclude significant contribution of the fac isomer, which is computed to lie about 10 kJ mol-1 higher in energy. We also address the possible presence of both meridional diastereomers and of higher energy conformers of meridional isomers. Finally, as expected for the d8 Ni2+-ion in an octahedral ligand environment, the IR spectrum also shows that the complexes are in a high-spin electron configuration.


Assuntos
Gases , Prótons , Gases/química , Ligantes , Espectrofotometria Infravermelho/métodos , Espectrometria de Massas
11.
J Chem Phys ; 157(15): 154103, 2022 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-36272795

RESUMO

Experimental and theoretical studies have highlighted protonated water clusters (PWCs) as important models of the excess proton in aqueous systems. A significant focus has been characterizing the spectral signatures associated with different excess proton solvation motifs. Accurate vibrational frequency calculations are crucial for connecting the measured spectra to the structure of PWCs. In this paper, we extend and characterize a coupled local mode (CLM) approach for calculating the infrared spectra of PWCs using the H+(H2O)4 cluster as a benchmark system. The CLM method is relatively low cost and incorporates the anharmonicity and coupling of OH vibrations. Here, we demonstrate the accuracy of the technique compared to experiments. We also illustrate the dependence of calculated spectral features on the underlying electronic structure theory and basis sets used in the local mode frequency and coupling calculations.


Assuntos
Prótons , Vibração , Espectrofotometria Infravermelho/métodos , Água/química , Modelos Teóricos
12.
Sci Rep ; 12(1): 17942, 2022 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-36289280

RESUMO

New Schiff base ligand, derived from antiviral valacyclovir, and its novel Cr(III), Mn(II), Co(II), Ni(II), Cu(II), Zn(II) complexes have been synthesized. By using a variety of analytical and spectroscopic techniques, the type of bonding between the ligand and the metal ions in the recently formed complexes was clarified. The Schiff base ligand act as a bidentate and coordinated with the metal ions through the azomethine-N and the phenolic-O centers, in a mono-deprotonated form. Except for the Zn(II) complex, which displayed a tetrahedral geometry, all complexes displayed octahedral geometry. The TGA findings supported that the stability and decomposition properties of the metal complexes were entirely distinct from one another. The thermogram showed decomposition of all investigated metal complexes above 200 °C in three, four or five steps, and indicated the high thermal stability of these complexes. According to XRD patterns, the particles of these complexes were located at the nanoscale. Moreover, for all the samples analyzed, the TEM images showed uniform and homogeneous surface morphology. The biological activity revealing the high efficiencies of the screened complexes as antibacterial and antitumor agents. The antimicrobial activity of the ligand and its complexes was examined against a variety of pathogenic bacteria and fungi including Escherichia coli, Staphylococcus aureus and Candida albicans. The data obtained revealed that the metal ion in the complexes enhanced the antimicrobial activity compared to the free ligand. The high efficiencies toward S. aureus, E. coli, and C. albicans appeared by Cu(II) complex 23, Ni(II) complex 20, and Ni(II) complex 19, respectively. The antitumor activity of the ligand and its complexes was tested against Hepatocellular carcinoma cell line (HepG-2 cells), the residue 28 which produced after heating the Cu(II) complex 25 at 200 °C for 1 h, exhibited strong inhibition of HepG-2 cell growth. The results of the DNA cleavage investigation demonstrated the ability of investigated Cu(II) complex to degrade DNA. The docking findings showed strong interactions of both the ligand and its examined Cu(II) complex, revealing their ability to cleavage DNA and their potent inhibitory effects on tumor cells. The electrical conductivity study confirmed that the ligand and its investigated complexes had semiconducting properties.


Assuntos
Antineoplásicos , Complexos de Coordenação , Bases de Schiff/química , Complexos de Coordenação/farmacologia , Complexos de Coordenação/química , Ligantes , Staphylococcus aureus , Escherichia coli/metabolismo , Valaciclovir/farmacologia , Antibacterianos/farmacologia , Antibacterianos/química , Metais/farmacologia , Candida albicans/metabolismo , Zinco/química , DNA/metabolismo , Íons/farmacologia , Antineoplásicos/farmacologia , Antivirais/farmacologia , Testes de Sensibilidade Microbiana , Espectrofotometria Infravermelho
13.
J Am Soc Mass Spectrom ; 33(11): 2165-2180, 2022 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-36279168

RESUMO

Uridine (Urd), a canonical nucleoside of RNA, is the most commonly modified nucleoside among those that occur naturally. Uridine has also been an important target for the development of modified nucleoside analogues for pharmaceutical applications. In this work, the effects of 5-halogenation of uracil on the structures and glycosidic bond stabilities of protonated uridine nucleoside analogues are examined using tandem mass spectrometry and computational methods. Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments and theoretical calculations are performed to probe the structural influences of these modifications. Energy-resolved collision-induced dissociation experiments along with survival yield analyses are performed to probe glycosidic bond stability. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of these species computed at the B3LYP/6-311+G(d,p) level of theory to determine the conformations experimentally populated. Spectral signatures in the IR fingerprint and hydrogen-stretching regions allow the 2,4-dihydroxy protonated tautomers (T) and O4- and O2-protonated conformers to be readily differentiated. Comparisons between the measured and predicted spectra indicate that parallel to findings for uridine, both T and O4-protonated conformers of the 5-halouridine nucleoside analogues are populated, whereas O2-protonated conformers are not. Variations in yields of the spectral signatures characteristic of the T and O4-protonated conformers indicate that the extent of protonation-induced tautomerization is suppressed as the size of the halogen substituent increases. Trends in the energy-dependence of the survival yield curves find that 5-halogenation strengthens the glycosidic bond and that the enhancement in stability increases with the size of the halogen substituent.


Assuntos
Halogenação , Nucleosídeos , Uridina/química , Prótons , Modelos Moleculares , Espectrofotometria Infravermelho/métodos , Halogênios
14.
J Phys Chem A ; 126(44): 8280-8294, 2022 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-36288121

RESUMO

Organic molecules, including α-hydroxyacids, are ubiquitous in the natural environment. Often found at water-air interfaces, organic molecules can alter the structure of the interface or participate in interfacial chemistry. Despite their prevalence in the environment, the structure and ordering of α-hydroxyacids have not been widely investigated at water-air interfaces, and the impact of the hydrophobic tail length on structure has not been explored. Here, for the first time, we use infrared reflection-absorption spectroscopy to assess the vibrational structure of α-hydroxyacids at a water surface as a function of surface partitioning and surface coverage. We study lactic acid, 2-hydroxyoctanoic acid, and 2-hydroxystearic acid, which have 1 carbon, 6 carbon, and 16 carbon tails, respectively. Vibrational features compared across the set of α-hydroxyacids studied here are used to determine the interaction of the polar headgroup with the water subphase and the ordering of the hydrophobic tail. We find that the carbonyl and α-hydroxyl groups participate in a complex hydrogen-bonding motif at the water-air interface that can be affected by the hydrophobic tail length and places the polar headgroup in or below the water-air interface. Furthermore, molecular ordering increases with the tail length or the surface coverage. The presence of the α-hydroxyl group causes the α-hydroxyacids to maintain a tilted orientation with respect to the surface normal even at high surface coverages. A combination of polar headgroup and hydrophobic tail effects dictates the overall orientation of α-hydroxyacids and can thus affect their ability to participate in chemistry and alter organic coatings on water surfaces.


Assuntos
Ar , Água , Água/química , Espectrofotometria Infravermelho/métodos , Ligação de Hidrogênio , Ácidos Carboxílicos , Carbono/química
15.
J Chem Phys ; 157(12): 124201, 2022 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-36182430

RESUMO

Time-resolved IR pump-probe (IR-PP) and two-dimensional IR (2D-IR) spectroscopy are valuable techniques for studying various ultrafast chemical and biological processes in solutions. The time-dependent changes of nonlinear IR signals reflecting fast molecular processes such as vibrational energy transfer and chemical exchange provide invaluable information on the rates and mechanisms of solvation dynamics and structural transitions of multispecies vibrationally interacting molecular systems. However, due to the intrinsic difficulties in distinguishing the contributions of molecule-specific processes to the time-resolved IR signals from those resulting from local heating, it becomes challenging to interpret time-resolved IR-PP and 2D-IR spectra exhibiting transient growing-in spectral components and cross-peaks unambiguously. Here, theoretical considerations of various effects of vibrational coupling, energy transfer, chemical exchange, the generation of hot ground states, molecular photothermal process, and their combinations on the line shapes and time-dependent intensities of IR-PP spectra and 2D-IR diagonal peaks and cross-peaks are presented. We anticipate that the present work will help researchers using IR pump-probe and 2D-IR techniques to distinguish local heating-induced photothermal signals from genuine nonlinear IR signals.


Assuntos
Vibração , Espectrofotometria Infravermelho/métodos
16.
Molecules ; 27(19)2022 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-36234809

RESUMO

We used two-dimensional infrared spectroscopy to disentangle the broad infrared band in the amide II vibrational regions of Bombyx mori native silk films, identifying the single amide II modes and correlating them to specific secondary structure. Amide I and amide II modes have a strong vibrational coupling, which manifests as cross-peaks in 2D infrared spectra with frequencies determined by both the amide I and amide II frequencies of the same secondary structure. By cross referencing with well-known amide I assignments, we determined that the amide II (N-H) absorbs at around 1552 and at 1530 cm-1 for helical and ß-sheet structures, respectively. We also observed a peak at 1517 cm-1 that could not be easily assigned to an amide II mode, and instead we tentatively assigned it to a Tyrosine sidechain. These results stand in contrast with previous findings from linear infrared spectroscopy, highlighting the ability of multidimensional spectroscopy for untangling convoluted spectra, and suggesting the need for caution when assigning silk amide II spectra.


Assuntos
Bombyx , Amidas/química , Animais , Seda , Espectrofotometria Infravermelho/métodos , Tirosina , Vibração
17.
Phys Chem Chem Phys ; 24(40): 24767-24783, 2022 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-36200672

RESUMO

Ultrafast two-dimensional infrared (2D-IR) spectroscopy of Escherichia coli Hyd-1 (EcHyd-1) reveals the structural and dynamic influence of the protein scaffold on the Fe(CO)(CN)2 unit of the active site. Measurements on as-isolated EcHyd-1 probed a mixture of active site states including two, which we assign to Nir-SI/II, that have not been previously observed in the E. coli enzyme. Explicit assignment of carbonyl (CO) and cyanide (CN) stretching bands to each state is enabled by 2D-IR. Energies of vibrational levels up to and including two-quantum vibrationally excited states of the CO and CN modes have been determined along with the associated vibrational relaxation dynamics. The carbonyl stretching mode potential is well described by a Morse function and couples weakly to the cyanide stretching vibrations. In contrast, the two CN stretching modes exhibit extremely strong coupling, leading to the observation of formally forbidden vibrational transitions in the 2D-IR spectra. We show that the vibrational relaxation times and structural dynamics of the CO and CN ligand stretching modes of the enzyme active site differ markedly from those of a model compound K[CpFe(CO)(CN)2] in aqueous solution and conclude that the protein scaffold creates a unique biomolecular environment for the NiFe site that cannot be represented by analogy to simple models of solvation.


Assuntos
Hidrogenase , Hidrogenase/química , Domínio Catalítico , Escherichia coli/metabolismo , Ligantes , Cianetos/química , Espectrofotometria Infravermelho/métodos , Proteínas
18.
Biomacromolecules ; 23(11): 4778-4785, 2022 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-36252236

RESUMO

Phytoglycogen (PG) is a polysaccharide produced in the kernels of sweet corn as soft, highly branched, compact nanoparticles. Its tree-like or dendritic architecture, combined with a high-safety profile, makes PG nanoparticles attractive for use in biological applications, many of which rely on the association or binding of small biomolecules. We have developed a methodology to functionalize surface plasmon resonance (SPR) sensor surfaces with PG nanoparticles, and we demonstrate the utility of the PG-functionalized SPR sensor by measuring the binding affinity of the tetrameric concanavalin A (ConA) protein to both native PG nanoparticles and smaller, softer acid-hydrolyzed PG nanoparticles. We measure comparable values of the equilibrium association constant K for native and acid-hydrolyzed PG, with a slightly smaller value for the acid-hydrolyzed particles that we attribute to unfavorable lateral interactions between the tetrameric subunits of ConA due to the increase in surface curvature of the smaller acid-hydrolyzed PG particles. We also use infrared reflection-absorption spectroscopy (IRRAS) to show that ConA maintains a large fraction of its native conformation, and thus its bioactivity, upon binding to PG, representing an important step toward the realization of PG as a novel bioactive delivery vehicle.


Assuntos
Nanopartículas , Ressonância de Plasmônio de Superfície , Concanavalina A/química , Ressonância de Plasmônio de Superfície/métodos , Nanopartículas/química , Espectrofotometria Infravermelho , Proteínas
19.
Nano Lett ; 22(20): 8060-8067, 2022 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-36214538

RESUMO

Dielectric metasurfaces governed by bound states in the continuum (BIC) are actively investigated for achieving high-quality factors and strong electromagnetic field enhancements. Traditional approaches reported for tuning the performance of quasi-BIC metasurfaces include tuning the resonator size, period, and structure symmetry. Here we propose and experimentally demonstrate an alternative approach through engineering slots within a zigzag array of elliptical silicon resonators. Through analytical theory, three-dimensional electromagnetic modeling, and infrared spectroscopy, we systematically investigate the spectral responses and field distributions of the slotted metasurface in the mid-IR. Our results show that by introducing slots, the electric field intensity enhancement near the apex and the quality factor of the quasi-BIC resonance are increased by a factor of 2.1 and 3.3, respectively, in comparison to the metasurface without slots. Furthermore, the slotted metasurface also provides extra regions of electromagnetic enhancement and confinement, which holds enormous potential in particle trapping, sensing, and emission enhancement.


Assuntos
Campos Eletromagnéticos , Silício , Vibração , Espectrofotometria Infravermelho , Eletricidade
20.
Phys Chem Chem Phys ; 24(42): 26046-26060, 2022 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-36268728

RESUMO

Halogenated groups are relevant in pharmaceutical applications and potentially useful spectroscopic probes for infrared spectroscopy. In this work, the structural dynamics and infrared spectroscopy of para-fluorophenol (F-PhOH) and phenol (PhOH) is investigated in the gas phase and in water using a combination of experiment and molecular dynamics (MD) simulations. The gas phase and solvent dynamics around F-PhOH and PhOH is characterized from atomistic simulations using empirical energy functions with point charges or multipoles for the electrostatics, Machine Learning (ML) based parametrizations and with full ab initio (QM) and mixed Quantum Mechanical/Molecular Mechanics (QM/MM) simulations with a particular focus on the CF- and OH-stretch region. The CF-stretch band is heavily mixed with other modes whereas the OH-stretch in solution displays a characteristic high-frequency peak around 3600 cm-1 most likely associated with the -OH group of PhOH and F-PhOH together with a characteristic progression below 3000 cm-1 due to coupling with water modes which is also reproduced by several of the simulations. Solvent and radial distribution functions indicate that the CF-site is largely hydrophobic except for simulations using point charges which renders them unsuited for correctly describing hydration and dynamics around fluorinated sites. The hydrophobic character of the CF-group is particularly relevant for applications in pharmaceutical chemistry with a focus on local hydration and interaction with the surrounding protein.


Assuntos
Fenóis , Teoria Quântica , Espectrofotometria Infravermelho/métodos , Água/química , Solventes/química , Fenol/química
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