Ring Breathing Research Articles

Study on the structure and two-dimensional correlation spectra of Cd(II) complexes based on flexible carboxylic ligands

A three-dimensional supramolecular reticular Cd(II) complex [Cd (PCPA) 2 (4,4′-bipy)]n was synthesized by hydrothermal method using PCPA and 4,4′-bipy as ligands. The structure of compound 1 was characterized by single crystal X-ray diffraction, elemental analysis, infrared spectroscopy, two-dimensional infrared correlation spectroscopy under thermal perturbation, thermogravimetric analysis and fluorescence spectroscopy. The results of single crystal X-ray diffraction analysis show that compound 1 belongs to monoclinic system and C2/c space group. Compound 1 forms a two-dimensional lamellar structure by bridging PCPA and 4,4 ′-bipy, and a three-dimensional supramolecular structure by π … π and C–H … π action. Two-dimensional infrared data of thermal perturbation show that the response peaks of flexible group νas (–CH2–) and unsaturated ν (Ar–H) to thermal perturbation are at 2936 cm−1, 3081 cm−1 and 3068 cm−1, but the response peaks of νas (–CH2–) are stronger than that ofν (=C–H) and more sensitive to temperature changes. The strong peak near 1590 cm−1 isν(benzene ring breathing) response to thermal perturbation, and the peak intensity is the largest. It is worth noting that the aromatic rings in compound 1 have C–H … π and π … π stacking, and these weak effects are sensitive to temperature changes, thus conducting the response to temperature changes to the aromatic rings, making the aromatic rings also sensitive to thermal perturbation. At the same time, the fluorescence properties of compound 1 were tested. Under 296 nm light excitation, the ligand PCPA has a strong emission peak at 313 nm and a weak acromion at 371 nm, which may be caused by the π*→π and weak π*→n transitions in the ligand, respectively. Under 369 nm light excitation, ligand 4,4′-bipy has a strong emission peak at 496 nm and a strong acromion at 459 nm.

Base-Pair Contents and Sequences of DNA Double Helices Differentiated by Surface-Enhanced Raman Spectroscopy.

Direct, label-free sequence analysis of DNA hybridization has been achieved by surface-enhanced Raman spectroscopy. In this work, aluminum-ion-aggregated and iodide-modified silver nanoparticles were used as substrates to obtain Raman spectra of the DNA strands with the same base composition but different sequences, which form random coils or various hairpin conformations. Upon DNA hybridization, reproducibly enhanced bands were easily observed, corresponding well to the formation of Watson-Crick hydrogen bonds, base ring breathing vibrations, and hairpin loops. These characteristic bands can be used to unambiguously distinguish the hairpins from the random DNA conformation. Moreover, by using the deoxyribose band (959 cm-1) as an internal standard to normalize the characteristic bands at 1703 cm-1 corresponding to the dG νC=O H bond, the guanine-cytosine base-pair contents and sequence in DNA hairpins can be accurately measured. Applying this method, a single base mutation in a functional double helix was confidently identified.

Plasmonic Gold Nanohole Array for Surface-Enhanced Raman Scattering Detection of DNA Methylation.

Surface-enhanced Raman spectroscopy (SERS), which utilizes nanogaps between noble-metal nanostructures as hot spots to yield ultrasensitive SERS signals, is an outstanding label-free and straightforward tool for DNA methylation analysis. Herein, a plasmonic gold nanohole array (PGNA) with well-controlled hot spots and an open surface was designed as a SERS substrate for DNA methylation detection. A finite-difference time-domain (FDTD) simulation was first employed to investigate the electric field distributions of the PGNA as a function of the geometric parameters. The plasmonic response was tuned to 785 cm-1 to match the ring breathing vibrational band of cytosine, the intensity change of which was revealed to be a marker of DNA methylation. Then, guided by the FDTD simulation results, the PGNA was fabricated via the electron beam lithography (EBL) technique. The fabricated PGNA had an open and easily accessible surface topology, a SERS enhancement factor of ∼106, and a relative standard deviation (RSD) of 7.1% for 500 repetitions over an area of 20 × 20 μm2 using 1 μM Rhodamine 6G as the Raman reporter. The fabricated PGNA was further used as a platform for determining DNA methylation. The proposed method exhibited a sensitivity for detecting 1% of methylation changes. Moreover, insight into the dynamic information on methylation events was obtained by combining principal component analysis (PCA) with 2D correlation spectroscopy analysis. Finally, clear discrimination of the different methylation sites, such as 5-methylcytosine and N6-methyladenine, was demonstrated.

Selective excitation of vibrational modes and probe for asymmetric intramolecular energy redistribution

Femtosecond time- and frequency-resolved coherent anti-Stokes Raman scattering spectroscopy was performed on liquid nitrobenzene (NB) to explore intramolecular vibrational energy redistribution in the electronic ground state. While high-frequency C–H stretching vibrational modes (vCH ∼ 3080 cm−1) were selectively excited, vibrational energy redistribution to the nitro group and phenyl ring breathing modes ( ∼ 1335 cm−1, ∼ 1514 cm−1 and ∼1584 cm−1) was described. While lower frequency modes of the nitro group and phenyl ring breathing were selectively excited, vibrational energy redistribution to C–H stretching modes with higher efficiency was detected. There is counter-intuitive vibrational energy flow in NB. Vibrational energy redistribution was discussed in the view of coherent population transfer between parent modes. Coherent coupling of these relevant modes and the selectivity of vibrational energy redistribution were further analyzed from the viewpoint of vibrational symmetry.

Potential dependent orientation of sulfanylbenzonitrile monolayers monitored by SERS

The change in orientation of 2-, 3-, and 4-sulfanylbenzonitrile (SBN) self assembled monolayers (SAMs) with respect to electrochemical potential was studied using surface-enhanced Raman spectroscopy (SERS). Being able to understand monolayer orientation under potential control has important applications in both sensors and molecular electronics, where orientation can affect sensitivity and electron transfer respectively. We characterise the vibrations of all three monolayers using a combination of experimental and density function theory (DFT) calculated spectra. The results reveal that the SERS intensities of both in plane (IP) and out of plane (OOP) modes of the aromatic ring and nitrile group are reversibly changed by potential, indicating an orientation change via variations in the tilt and/or twist angles. At more negative potentials the nitrile group of all three SAMs is more perpendicular to the electrode surface and at more positive potentials it is more parallel, governed by an electrostatic interaction between the nitrile group and the electrode surface. Additional effects of the applied potential are observed for the orientation of the ring with respect to the electrode surface through aromatic ring-surface π interactions, confirmed by examination of the effects of the applied potential on the peak width of the CC ring breathing mode.

Micro-Raman imaging of isomeric segregation in small-molecule organic semiconductors

Charge transport in organic semiconductors is highly sensitive to film heterogeneity and intermolecular interactions, but probing these properties on the length scales of disorder is often difficult. Here we use micro-Raman spectroscopy to assign vibrational modes of isomerically pure syn and anti 2,8-difluoro-5,11-bis(triethylsilylethynyl)anthradithiophene (diF-TES ADT) by comparing to density functional theory calculations. With polarization-dependent measurements, we determine the orientation of crystallites in pure isomers. In mixed-isomer samples, we observe narrow linewidths and superposition spectra, indicating coexistence of isomerically pure sub-domains on length scales smaller than the probe area. Using the ring breathing modes close to 1300 cm−1 as indicators of the pure isomer crystalline sub-domains, we image their spatial distribution with 200-nm resolution. These results demonstrate the power of micro-Raman spectroscopy for investigating spatial heterogeneities and clarifying the origin of the reduced charge carrier mobility displayed in mixed-isomer diF-TES ADT.

Probing Electrolyte Solvents at Solid/Liquid Interface Using Gap-Mode Surface-Enhanced Raman Spectroscopy

Understanding the aprotic solution structures at the immediate vicinity of solid/liquid interface (SLI) is critically important for next generation lithium ion battery development. Yet, it is still challenging to investigate the carbonate chemical profiles close to the diffuse layer (about 10 nm) of the electrical double layer at SLI due to the lack of a ultrahigh surface sensitive tool. In this work, we demonstrate the structures of commonly used carbonate solvents (ethylene carbonate (EC) and diethyl carbonate (DEC)) and a carbonate additive (fluoroethylene carbonate (FEC)) in a commercial Li-ion battery electrolyte can be determined at ∼17 nm above the electrode surface. This is only enabled by a nanogap surface-enhanced Raman spectroscopy (SERS) technique based on a monolayer gold nanoparticle (Au NP) ensemble. The SERS enhancement factor (EF) of those carbonates was found to depend on the molecular polarizability, with the maximum EF at ∼105 found for EC and FEC. Despite their alike chemical structures, this monolayer Au NP SERS substrate is fully capable of discrimiating the different Raman finger prints of EC and FEC. Compared to EC, several vibration modes in FEC, such as C-C skeletal deformation, ring breathing band and C=O stretching band, shift to higher frequencies because of the displacement of a hydrogen atom by a much heavier fluorine atom in a methylene bridge. This counterintuitive observation against the commonly used “ball and spring” model in vibrational spectroscopy is mostly due to the increased bond strength in the FEC ring versus that of EC. A second order empirical polynomial best describes the correlation between the SERS band integration of EC or DEC molar concentration. Our findings open up new opportunities for in-depth understanding of the electrolyte molecular vibrational behaviors at direct solid/liquid interface and developing advanced electrolytes for next generation lithium-ion batteries.

Raman spectra of aqueous uracil stacked dimer: First principle molecular dynamics simulation

Raman spectra of aqueous uracil stacked dimer have been studied by employing density functional theory based molecular dynamics simulation together with the maximally localized Wannier functions. The unpolarized spectra are in a reasonable good agreement with the available experimental spectrum. The discrepancies are attributed to the used density functional approximation. Static quantum chemical calculations reveal that the coupling of the carbonyl stretching modes is significantly weaker than the one of the amide modes. The noncoincidence effect of the ring breathing mode is explained in terms of repulsive steric interactions.

A SERS-based molecular sensor for selective detection and quantification of copper(II) ions

A novel SERS-based molecular sensor for detection and quantification of copper(II) ions with very good specificity and selectivity is reported in this work. The sensing is enabled by the employment of a synthesized dipicolylamine-based ligand anchored onto plasmonic gold nanoparticles through the sulfur atom of the methylthio group. The interaction of the ligand with copper(II) ions is followed by changes in the spectral features associated with pyridine ring breathing, as indicated by quantum chemical calculations performed at the density functional level of theory, which are proportional to the copper(II) concentration. The detection of copper(II) was possible down to 5 × 10−8 M in water. The proposed molecular sensor was applied for the detection of copper(II) ions in white wine, with the ability to detect amounts of copper(II) in wine lower than the maximum recommended amount of 7.87 × 10−6 M (0.5 μg/mL), indicating that the proposed molecular sensor is of potential interest as a routine test for the control of the copper(II) content in wine during wine production and in the final product.

Structural Features of DNA G-Quadruplexes Revealed by Surface-Enhanced Raman Spectroscopy.

Surface-enhanced Raman spectroscopy (SERS) has been successfully used for the label-free detection of single-stranded oligonucleotides. However, the detection of complex DNA secondary structures remains a challenge. Structural features of diverse DNA G-quadruplexes were investigated via a novel SERS method. As a result, a series of highly reproducible and sensitive SERS signatures featuring the structures of G-quadruplexes were obtained. For the first time, we reported remarkably enhanced SERS bands corresponding to purine ring breathing vibrations. Moreover, we observed that by measuring the intensity of the bands corresponding to intramolecular hydrogen bonds, we could quantitatively assess the stability of the G-quadruplexes. Because no labels on DNA strands were present as the experiments were carried out in the solution, the fingerprint peaks reflect the native, internal structure of the G-quadruplexes accurately. The method here detailed provides new insights into the promising applications of diverse DNA structural studies.

Isomerization Reaction of mer- to fac-Tris(2-phenylpyridinato-N,C2')Iridium(III) Monitored by Using Surface-Enhanced Raman Spectroscopy.

We developed a new method by enclosing the complex tris(2-phenylpyridinato-N,C2')Iridium(III), Ir(ppy)3 with surfactant cetyltrimethylammonium bromide (CATB), coated with a thin layer of silica then bonded to the surface of silver nanoparticle. These samples were used to acquire surface-enhanced Raman scattering (SERS) spectra. The thickness of silica layer was controlled to have efficient phosphorescence quenching and Raman enhancement by metal nanoparticle. The SERS spectra of fac- and mer-Ir(ppy)3, recorded at 633 nm excitation, display distinct ring breathing mode features because the total symmetric vibrational bands were enhanced. This provides a convenient means to differentiate these isomers with great sensitivity and to study their isomerization process. A direct conversion reaction of mer- to fac- isomerization is identified with time constant 3.1 min when mer was irradiated with Xe light. Via thermal activation, under moderate conditions (pH 5.5 and 343 K), we observed an intermediate particularly with new bands 320/662 cm-1 after heating for 17.5 h, and then those bands disappeared to form fac-Ir(ppy)3. On the basis of DFT calculations, the intermediate is proposed to contain octahedral N-N Ir(ppy)3-HO-silica structure; band at 320 cm-1 is assigned to iridium oxygen stretching mode νIr-O of this intermediate. Under acidic conditions, pH 1-2 catalyzed by silanol in silica, byproduct with band at 353 cm-1 was observed. According to the SERS bands and the calculation, this byproduct is assigned to be iridium(III) siloxide, and the new band is assigned to νIr-O.

Discrimination between hydrogen bonding and protonation in the spectra of a surface-enhanced Raman sensor.

We investigate the surface-enhanced Raman spectra of 4-mercaptopyridine on gold in a variety of acids. 4-Mercaptopyridine is a known pH sensor which exhibits characteristic spectral changes when the pH is changed. Here we show with the help of experiment and density functional calculations that the ring breathing mode is also highly sensitive to hydrogen bonding. Its spectral signature is a broad band with up to three contributions from free, protonated and hydrogen-bonded 4-mercaptopyridine. Unlike pyridine in solution, where protonation leads to a higher ring breathing frequency than hydrogen-bonding, we find that protonated adsorbed 4-mercaptopyridine possesses a frequency which is lower than the corresponding hydrogen-bonded species. The Raman spectra indicate an orientation change of the aromatic ring in acidic solutions, which could be caused by a cation/π interaction between protonated and deprotonated 4-mercaptopyridine. As the frequencies of the three species are well separated, adsorbed 4-mercaptopyridine can probe more complex changes in the solution environment than just pH.

Selective Suppression of Stimulated Raman Scattering with Another Competing Stimulated Raman Scattering.

A three-beam femtosecond stimulated Raman scattering (SRS) scheme is formulated and demonstrated to simultaneously induce two different SRS processes associated with Raman-active modes in the same molecule. Two SR gains involving a common pump pulse are coupled and compete: As one of the Stokes beam intensities increases, the other SRS is selectively suppressed. We provide theoretical description and experimental evidence that the selective suppression behavior is due to the limited number of pump photons used for both of the two SRS processes when an intense depletion beam induces one SRS process. The maximum suppression efficiency was ∼60% with our experimental setup, where the SR gain of the ring breathing mode of benzene is the target SRS signal, which is allowed to compete with another SRS process, induced by an intense depletion beam, of the CH stretching mode. We anticipate a potential of this new switching-off concept in super-resolution label-free microscopy.

Investigation of reactive and spectroscopic properties of oxobutanoic acid derivative: Combined spectroscopic, DFT, MD and docking study

The optimized geometry and wavenumbers of 4-[(4-acetylphenyl)amino]-2-methylidene-4-oxobutanoic acid (APAMOB) have been calculated by density functional theory (DFT) using Becke's three-parameters hybrid functional (B3LYP) with 6–311++G(d) (5D, 7F) basis set. The theoretically predicted vibrational wavenumbers were compared with the observed FT-IR and FT-Raman spectra. The NH stretching wavenumber is red shifted in the IR spectrum from the computed wavenumber, which indicates the weakening of the NH bond. The ring breathing mode of the para substituted phenyl ring is assigned at 836 cm−1 experimentally and at 835 cm−1 theoretically. Molecular electrostatic potential map has also been plotted for predicting the reactive sites in the molecule. Using natural bond orbitals analysis hyperconjugative interactions and second order stabilization energies are calculated. Nonlinear optical properties of the molecule are predicted. In order to determine molecule sites that could be sensitive towards electrophilic attacks we have calculated ALIE values and mapped them to electron density surface. In the same way we have also visualized Fukui functions, which helped us to further gain an insight into the local reactivity properties of title molecule. Bond dissociation energies (BDE) have been calculated in order to determine if autoxidation mechanism is possible, while the potential influence of hydrolysis was investigated to calculations of radial distribution functions (RDF) obtained after molecular dynamics (MD) simulations. Molecular docking study suggests that the title compound shows the inhibitory activity against 2-deoxy-d-gluconate 3-dehydrogenase.

Synthesis, XRD single crystal structure analysis, vibrational spectral analysis, molecular dynamics and molecular docking studies of 2-(3-methoxy-4-hydroxyphenyl) benzothiazole

The vibrational spectra and corresponding vibrational assignments of 2-(3-methoxy-4-hydroxyphenyl)benzothiazole is reported. Single crystal XRD data of the title compound is reported and the orientation of methoxy group is cis to nitrogen atom of the thiazole ring. The phenyl ring breathing modes of the title compound are assigned at 1042 and 731 cm−1 theoretically. The charge transfer within the molecule is studied using frontier molecular orbital analysis. The chemical reactivity descriptors are calculated theoretically. The NMR spectral data predicted theoretically are in good agreement with the experimental data. The strong negative region spread over the phenyl rings, nitrogen atom and oxygen atom of the hydroxyl group in the MEP plot is due to the immense conjugative and hyper conjugative resonance charge delocalization of π-electrons. Molecule sites prone to electrophilic attacks have been determined by analysis of ALIE surfaces, while Fukui functions provided further insight into the local reactivity properties of title molecule. Autoxidation properties have been investigated by calculation of bond dissociation energies (BDEs) of hydrogen abstraction, while BDEs of the rest of the single acyclic bonds were valuable for the further investigation of degradation properties. Calculation of radial distribution functions was performed in order to determine which atoms of the title molecule have pronounced interactions with water molecules. The title compound forms a stable complex with aryl hydrocarbon receptor and can be a lead compound for developing new anti-tumor drug. Antimicrobial properties of the title compound was screened against one bacterial culture Escherchia coli and four fungal cultures viz., Aspergillus niger, Pencillum chrysogenum, Saccharomyces cerevisiae and Rhyzopus stolonifer.

Distinct properties of the triplet pair state from singlet fission.

Singlet fission, the conversion of a singlet exciton (S1) to two triplets (2 × T1), may increase the solar energy conversion efficiency beyond the Shockley-Queisser limit. This process is believed to involve the correlated triplet pair state 1(TT). Despite extensive research, the nature of the 1(TT) state and its spectroscopic signature remain actively debated. We use an end-connected pentacene dimer (BP0) as a model system and show evidence for a tightly bound 1(TT) state. It is characterized in the near-infrared (IR) region (~1.0 eV) by a distinct excited-state absorption (ESA) spectral feature, which closely resembles that of the S1 state; both show vibronic progressions of the aromatic ring breathing mode. We assign these near-IR spectra to 1(TT)→Sn and S1→Sn' transitions; Sn and Sn' likely come from the antisymmetric and symmetric linear combinations, respectively, of the S2 state localized on each pentacene unit in the dimer molecule. The 1(TT)→Sn transition is an indicator of the intertriplet electronic coupling strength, because inserting a phenylene spacer or twisting the dihedral angle between the two pentacene chromophores decreases the intertriplet electronic coupling and diminishes this ESA peak. In addition to spectroscopic signature, the tightly bound 1(TT) state also shows chemical reactivity that is distinctively different from that of an individual T1 state. Using an electron-accepting iron oxide molecular cluster [Fe8O4] linked to the pentacene or pentacene dimer (BP0), we show that electron transfer to the cluster occurs efficiently from an individual T1 in pentacene but not from the tightly bound 1(TT) state. Thus, reducing intertriplet electronic coupling in 1(TT) via molecular design might be necessary for the efficient harvesting of triplets from intramolecular singlet fission.

Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics.

The ability to detect changes in the local environment of proteins is pivotal to determining their dynamic nature during many biological processes. For this purpose, the utility of the tyrosine ring breathing vibration as a sensitive infrared reporter for measuring the local electric field in protein is investigated. Variations in the bandwidth of this vibrational transition in a variety of solvents indicate differences in microenvironment affect the inhomogeneous broadening and thus the frequency distribution. The ring mode is influenced by direct and indirect interactions associated with the charge distribution of the surrounding solvent molecules. Molecular dynamics simulations were implemented to obtain a correlation between the electric field induced by the solvent on the mode and the observed vibrational bandwidth. Moreover, the Trp-cage was synthesized as a model peptide system to access the efficacy of the correlation to predict the electric field strength within the hydrophobic core of the native and denatured states of the protein. The 2D IR spectra of tyrosine in dimethyl sulfoxide (DMSO) and water (D2O) show a two-fold difference in the time constant of the vibrational dynamics alluding to the dephasing mechanisms of the vibration and supporting the model put forth about the solvachromatic nature of the transition.

Conformational, vibrational and DFT studies of a newly synthesized arylpiperazine-based drug and evaluation of its reactivity towards the human GABA receptor

This study reports a computational assessment of important biochemical properties and vibrational assignments for the synthesized 1-(4-(3-methoxy-4-nitrophenyl)piperazin-1-yl)ethanone (MNPE). MNPE is related to the commonly used arylpiperazine-based drugs that exhibit a wide range of pharmacological activities. The characterization of MNPE is based on the readily sighted 1363 cm−1 infrared band (associated with piperazine ring stretching), 1308 cm−1 Raman line (associated with the phenyl ring breathing), 1242 cm−1 Raman line and 1092 cm−1 infrared band (both associated with CN stretching) as key modes in its vibrational spectra. First principle calculations revealed that MNPE could exist in sixteen different plausible conformations, which were used as basis to understand the possible molecular docking mechanism of the molecule as an agonist in the human GABAA receptor. The best binding scenarios showed the presence of intramolecular hydrogen bonding in MNPE and was comparable with the most stable configuration. It was further evaluated for its reactivity properties by utilizing the concepts of Average Local Ionization Energies (ALIE) and Fukui functions. The autoxidation and hydrolysis degradation likelihood of MNPE estimated from the computed bond dissociation energies and radial distribution functions predicted that MNPE is to be readily biodegradable in aqueous solutions.

Optical nonlinearity and charge transfer analysis of pyrene adsorbed on silver: Computational and experimental investigations

The interaction of pyrene on silver has been investigated using both experimental and computational methods. Hyperpolarizabilities computed theoretically together with experimental nonlinear absorption from open aperture Z-scan measurements, point towards a possible use of pyrene adsorbed on silver in the rational design of NLO devices. Presence of a red shift in both simulated and experimental UV–Vis spectra confirms the adsorption on silver, which is due to the electrostatic interaction between silver and pyrene, inducing variations in the structural parameters of pyrene. Fukui calculations along with MEP plot predict the electrophilic nature of the silver cluster in the presence of pyrene, with NBO analysis revealing that the adsorption causes charge redistribution from the first three rings of pyrene towards the fourth ring, from where the 2p orbitals of carbon interact with the valence 5s orbitals of the cluster. This is further confirmed by the downshifting of ring breathing modes in both the experimental and theoretical Raman spectra.

Modification of benzoxazole derivative by bromine-spectroscopic, antibacterial and reactivity study using experimental and theoretical procedures

N-[2-(2-bromophenyl)-1,3-benzoxazol-5-yl]-2-phenylacetamide (NBBPA) was synthesized in this study as an original compound in order to evaluate its antibacterial activity against representative Gram-negative and Gram-positive bacteria, with their drug-resistant clinical isolate. Microbiological results showed that this compound had moderate antibacterial activity. Study also encompassed detailed FT-IR, FT-Raman and NMR experimental and theoretical spectroscopic characterization and assignation of the ring breathing modes of the mono-, ortho- and tri-substituted phenyl rings is in agreement with the literature data. DFT calculations were also used to identify specific reactivity properties of NBBPA molecule based on the molecular orbital, charge distribution and electron density analysis, which indicated the reactive importance of carbonyl and NH2 groups, together with bromine atom. DFT calculations were also used for investigation of sensitivity of the NBBPA molecules towards the autoxidation mechanism, while molecular dynamics (MD) simulations were used to investigate the influence of water. The molecular docking results suggest that the compound might exhibit inhibitory activity against GyrB complex.