The hydrogen-bonding dynamics of water to a nitrile-functionalized electrode is modulated by voltage according to ultrafast 2D IR spectroscopy.

We report the hydrogen-bonding dynamics of water to a nitrile-functionalized and plasmonic electrode surface as a function of applied voltage. The surface-enhanced two-dimensional infrared spectra exhibit hydrogen-bonded and non-hydrogen-bonded nitrile features in similar proportions, plus cross peaks between the two. Isotopic dilution experiments show that the cross peaks arise predominantly from chemical exchange between hydrogen-bonded and non-hydrogen-bonded nitriles. The chemical exchange rate depends upon voltage, with the hydrogen bond of the water to the nitriles breaking 2 to 3 times slower (>63 vs. 25 ps) under a positive as compared to a negative potential. Spectral diffusion created by hydrogen-bond fluctuations occurs on a ~1 ps timescale and is moderately potential-dependent. Timescales from molecular dynamics simulations agree qualitatively with the experiment and show that a negative voltage causes a small net displacement of water away from the surface. These results show that the voltage applied to an electrode can alter the timescales of solvent motion at its interface, which has implications for electrochemically driven reactions.

Zn Single-Atom Catalysts Enable the Catalytic Transfer Hydrogenation of α,ß-Unsaturated Aldehydes.

Highly active nonprecious-metal single-atom catalysts (SACs) toward catalytic transfer hydrogenation (CTH) of α,ß-unsaturated aldehydes are of great significance but still are deficient. Herein, we report that Zn-N-C SACs containing Zn-N3 moieties can catalyze the conversion of cinnamaldehyde to cinnamyl alcohol with a conversion of 95.5% and selectivity of 95.4% under a mild temperature and atmospheric pressure, which is the first case of Zn-species-based heterogeneous catalysts for the CTH reaction. Isotopic labeling, in situ FT-IR spectroscopy, and DFT calculations indicate that reactants, coabsorbed at the Zn sites, proceed CTH via a "Meerwein-Ponndorf-Verley" mechanism. DFT calculations also reveal that the high activity over Zn-N3 moieties stems from the suitable adsorption energy and favorable reaction energy of the rate-determining step at the Zn active sites. Our findings demonstrate that Zn-N-C SACs hold extraordinary activity toward CTH reactions and thus provide a promising approach to explore the advanced SACs for high-value-added chemicals.

Optimized infrared spectrum of ( H 2 O ) m : ( H C N ) n $$ {\left({H}_2O\right)}_m:{(HCN)}_n $$ mixtures.

Using density functional theory at D3-B3LYP/aug-cc-pVDZ level combined with the conductor-like polarizable continuum model (CPCM) solvent model, a study of the IR spectrum of H 2 O $$ {\mathrm{H}}_2\mathrm{O} $$ :HCN mixtures is reported. The CPCM solvent effect notably enhances the accuracy of the IR spectra compared to gas-phase calculations, while the dielectric constant value has minimum impact on the final spectrum. An optimized methodology is suggested that effectively minimizes the root mean square deviation between theoretical and experimental data. This novel approach not only enhances the quality of the final IR spectra but also captures relevant spectral features, highlighting its potential to decipher molecular interactions in such intricate mixtures.

Spectral and conformational characteristics of phycocyanin associated with changes of medium pH.

C-phycocyanin (C-PC) is the main component of water-soluble light-harvesting complexes (phycobilisomes, PBS) of cyanobacteria. PBS are involved in the absorption of quantum energy and the transfer of electronic excitation energy to the photosystems. A specific environment of C-PC chromophoric groups is provided by the protein matrix structure including protein-protein contacts between different subunits. Registration of C-PC spectral characteristics and the fluorescence anisotropy decay have revealed a significant pH influence on the chromophore microenvironment: at pH 5.0, a chromophore is more significantly interacts with the solvent, whereas at pH 9.0 the chromophore microenvironment becomes more viscous. Conformations of chromophores and the C-PC protein matrix have been studied by Raman and infrared spectroscopy. A decrease in the medium pH results in changes in the secondary structure either the C-PC apoproteins and chromophores, the last one adopts a more folded conformation.

Probing calmodulin-NO synthase interactions via site-specific infrared spectroscopy: an introductory investigation.

Calmodulin (CaM) binds to a linker between the oxygenase and reductase domains of nitric oxide synthase (NOS) to regulate the functional conformational dynamics. Specific residues on the interdomain interface guide the domain-domain docking to facilitate the electron transfer in NOS. Notably, the docking interface between CaM and the heme-containing oxygenase domain of NOS is isoform specific, which is only beginning to be investigated. Toward advancing understanding of the distinct CaM-NOS docking interactions by infrared spectroscopy, we introduced a cyano-group as frequency-resolved vibrational probe into CaM individually and when associated with full-length and a bi-domain oxygenase/FMN construct of the inducible NOS isoform (iNOS). Site-specific, selective labeling with p-cyano-L-phenylalanine (CNF) by amber suppression of CaM bound to the iNOS has been accomplished by protein coexpression due to the instability of recombinant iNOS protein alone. We introduced CNF at residue 108, which is at the putative CaM-heme (NOS) docking interface. CNF was also introduced at residue 29, which is distant from the docking interface. FT IR data show that the 108 site is sensitive to CaM-NOS complex formation, while insensitivity to its association with the iNOS protein or peptide was observed for the 29 site. Moreover, narrowing of the IR bands at residue 108 suggests the C≡N probe experiences a more limited distribution of environments, indicating side chain restriction apparent for the complex with iNOS. This initial work sets the stage for residue-specific characterizations of structural dynamics of the docked states of NOS proteins.

Aggregation of N-Heteropolycyclic Aromatic Molecules: The Acridine Dimer and Trimer.

Polycyclic aromatic hydrocarbons and their nitrogen-substituted analogues are of great interest for various applications in organic electronics. The performance of such devices is determined not only by the properties of the single molecules, but also by the structure of their aggregates, which often form via self-aggregation. Gaining insight into such aggregation processes is a challenging task, but crucial for a fine-tuning of the materials properties. In this work, an efficient approach for the generation and characterisation of aggregates is described, based on matrix-isolation experiments and quantum-chemical calculations. This approach is exemplified for aggregation of acridine. The acridine dimer and trimer are thoroughly analysed on the basis of experimental and calculated UV and IR absorption spectra, which agree well with each other. Thereby a novel structure of the acridine dimer is found, which disagrees with a previously reported one. The calculations also show the changes from excitonic coupling towards orbital interactions between two molecules with decreasing distance to each other. In addition, a structure of the trimer is determined. Finally, an outlook is given on how even higher aggregates can be made accessible through experiment.

Investigation of Isolated IrF5 -, IrF6 - Anions and M[IrF6] (M=Na, K, Rb, Cs) Ion Pairs by Matrix-Isolation Spectroscopy and Relativistic Quantum-Chemical Calculations.

The molecular IrF5 -, IrF6 - anions and M[IrF6] (M=Na, K, Rb, Cs) ion pairs were prepared by co-deposition of laser-ablated alkali metal fluorides MF with IrF6 and isolated in solid neon or argon matrices under cryogenic conditions. The free anions were obtained as well by co-deposition of IrF6 with laser-ablated metals (Ir or Pt) as electron sources. The products were characterized in a combined analysis of matrix IR spectroscopy and electronic structure calculations using two-component quasi-relativistic DFT methods accounting for spin-orbit coupling (SOC) effects as well as multi-reference configuration-interaction (MRCI) approaches with SOC. Inclusion of SOC is crucial in the prediction of spectra and properties of IrF6 - and its alkali-metal ion pairs. The observed IR bands and the computations show that the IrF6 - anion adopts an Oh structure in a nondegenerate ground state stabilized by SOC effects, and not a distorted D4h structure in a triplet ground state as suggested by scalar-relativistic calculations. The corresponding "closed-shell" M[IrF6] ion pairs with C3v symmetry are stabilized by coordination of an alkali metal ion to three F atoms, and their structural change in the series from M=Na to Cs was proven spectroscopically. There is no evidence for the formation of IrF7, IrF7 - or M[IrF7] (M=Na, K, Rb, Cs) ion pairs in our experiments.

Enhanced Orientation of Liquid Crystals Inside Micropores of Metal-Organic Frameworks Having Thermoresponsivity.

With the aim of controlling the orientation of liquid crystals (LCs) toward realizing external stimuli-responsive materials with tunable functionalities, we synthesized a composite of LCs and metal-organic frameworks (MOFs) by filling LCs into the pores of MOFs (LC@MOFs) for the first time. The included LCs interact with the MOFs through coordination bonds between the cyano groups of the LCs and the metal ions of the MOFs, enabling the orientation of the LC molecules inside the pores of the MOFs and the realization of birefringence of LC@MOFs. The three-dimensional nanometer interstice frameworks maintained the LC orientation even at temperatures much higher than the isotropic phase transition temperature of bulk LCs. Furthermore, the orientational state changed upon heating or cooling, inducing temperature-dependent birefringence. This study provides a new approach to the development of stimuli-responsive optical materials and stimuli-responsive MOFs.

Exploring the Influence of the Phosphorus-Heteroatom Substitution in Nicotine on Its Electronic and Vibrational Spectroscopic Properties.

The influence of phosphorus substitution of nitrogen in heterocyclic compounds on the vibrational spectroscopy as well as frontier molecular orbitals are analyzed. Nicotine with two nitrogen atoms in its structure is taken as the sample system to be studied computationally. By replacing the nitrogen atom in one or both rings of this molecule with phosphorus, three nicotine derivatives are created. The vibrational circular dichroism and infrared spectra of these four molecules in their monomer state, as well as the assemblies up to trimers are determined. The aforementioned spectra are calculated using static quantum chemical calculations employing a cluster-weighted approach. The calculated gas phase spectra of nicotine are compared to their respective experimental spectra. It is observed that the nicotine derivatives with phosphorus in the methylpyrrolidine ring have considerably different gas phase and bulk phase vibrational circular dichroism spectra when compared to nicotine. The phosphorus substitution reduces the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital as well as altering the polarizability and reactivity of the investigated molecules.

Biomolecular fingerprints of the effect of zoledronic acid on prostate cancer stem cells: Comparison of 2D and 3D cell culture models.

Revealing the potential of candidate drugs against different cancer types without disrupting normal cells depends on the drug mode of action. In the current study, the drug response of prostate cancer stem cells (PCSCs) to zoledronic acid (ZOL) grown in two-dimensional (2D) and three-dimensional (3D) culture systems was compared using Fourier transform-infrared (FT-IR) spectroscopy which is a vibrational spectroscopic technique, supporting by biochemical assays and imaging techniques. Based on our data, in 2D cell culture conditions, the ZOL treatment of PCSCs isolated according to both C133 and CD44 cell surface properties induced early/late apoptosis and suppressed migration ability. The CD133 gene expression and protein levels were altered, depending on culture systems. CD133 expression was significantly reduced in 2D cells upon ZOL treatment. FT-IR data revealed that the integrity, fluidity, and ordering/disordering states of the cell membrane and nucleic acid content were altered in both 2D and 3D cells after ZOL treatment. Regular protein structures decrease in 2D cells while glycogen and protein contents increase in 3D cells, indicating a more pronounced cytotoxic effect of ZOL for 2D cells. Untreated 3D PCSCs exhibited an even different spectral profile associated with IR signals of lipids, proteins, nucleic acids, and glycogen in comparison to untreated 2D cells. Our study revealed significant differences in the drug response and cellular constituents between 2D and 3D cells. Exploring molecular targets and/or drug-action mechanisms is significant in cancer treatment approaches; thus, FT-IR spectroscopy can be successfully applied as a novel drug-screening method in clinical research.

Role of Constituent Oxides for Thermal Mineralization of o-Dichloro Benzene over Mixed-Oxide-TiO2 Catalysts: A Mechanistic Explanation.

Catalysts with V2O5, WO3 and V2O5-WO3 dispersed over TiO2 were synthesized using sol-gel technique and thoroughly characterized by various techniques. The catalysts were evaluated for degradation of ortho-dichloro benzene (o-DCB) in air/helium, a representative probe molecule for polychlorinated dibenzo-para-dioxin and polychlorinated dibenzofuran by employing in situ Fourier-transform infrared spectroscopy (FT-IR spectroscopy). Different intermediate species formed on the surface of the TiO2 supported catalysts through of interaction of sorbate molecules with the lattice and/or gaseous oxygen were investigated in detail. Analysis of vibrational bands, observed during sorption of o-DCB and o-DCB-air mixture as a function of temperature over these catalysts, delineated the role of surface intermediate species such as phenolate, enolates, maleates, carboxylates, carbonates in mineralization of o-DCB. Nature and stability of intermediate species, found to be different over these catalysts, were able to elucidate the catalytic activity trend.

Single-Particle Analysis of the Photodegradation of Submicron Polystyrene Particles Using Infrared Photothermal Heterodyne Imaging.

Sunlight irradiation is the predominant process for degrading plastics in the environment, but our current understanding of the degradation of smaller, submicron (<1000 nm) particles is limited due to prior analytical constraints. We used infrared photothermal heterodyne imaging (IR-PHI) to simultaneously analyze the chemical and morphological changes of single polystyrene (PS) particles (∼1000 nm) when exposed to ultraviolet (UV) irradiation (λ = 250-400 nm). Within 6 h of irradiation, infrared bands associated with the backbone of PS decreased, accompanied by a reduction in the particle size. Concurrently, the formation of several spectral features due to photooxidation was attributed to ketones, carboxylic acids, aldehydes, esters, and lactones. Spectral outcomes were used to present an updated reaction scheme for the photodegradation of PS. After 36 h, the average particle size was reduced to 478 ± 158 nm. The rates of size decrease and carbonyl band area increase were -24 ± 3.0 nm h-1 and 2.1 ± 0.6 cm-1 h-1, respectively. Using the size-related rate, we estimated that under peak terrestrial sunlight conditions, it would take less than 500 h for a 1000 nm PS particle to degrade to 1 nm.

Raman spectroscopy is a powerful tool in molecular paleobiology: An analytical response to Alleon et al. (https://doi.org/10.1002/bies.202000295).

A recent article argued that signals from conventional Raman spectroscopy of organic materials are overwhelmed by edge filter and fluorescence artefacts. The article targeted a subset of Raman spectroscopic investigations of fossil and modern organisms and has implications for the utility of conventional Raman spectroscopy in comparative tissue analytics. The inferences were based on circular reasoning centered around the unconventional analysis of spectra from just two samples, one modern, and one fossil. We validated the disputed signals with in situ Fourier-Transform Infrared (FT-IR) Spectroscopy and through replication with different lasers, filters, and operators in independent laboratories. Our Raman system employs a holographic notch filter which is not affected by edge filter or other artefacts. Multiple lines of evidence confirm that conventional Raman spectra of fossils contain biologically and geologically meaningful information. Statistical analyses of large Raman and FT-IR spectral data sets reveal patterns in fossil composition and yield valuable insights into the history of life.

AI-based spectroscopic monitoring of real-time interactions between SARS-CoV-2 and human ACE2.

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), invades a human cell via human angiotensin-converting enzyme 2 (hACE2) as the entry, causing the severe coronavirus disease (COVID-19). The interactions between hACE2 and the spike glycoprotein (S protein) of SARS-CoV-2 hold the key to understanding the molecular mechanism to develop treatment and vaccines, yet the dynamic nature of these interactions in fluctuating surroundings is very challenging to probe by those structure determination techniques requiring the structures of samples to be fixed. Here we demonstrate, by a proof-of-concept simulation of infrared (IR) spectra of S protein and hACE2, that time-resolved spectroscopy may monitor the real-time structural information of the protein-protein complexes of interest, with the help of machine learning. Our machine learning protocol is able to identify fine changes in IR spectra associated with variation of the secondary structures of S protein of the coronavirus. Further, it is three to four orders of magnitude faster than conventional quantum chemistry calculations. We expect our machine learning protocol would accelerate the development of real-time spectroscopy study of protein dynamics.

Short-lived intermediate in N2O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography.

Nitric oxide (NO) reductase from the fungus Fusarium oxysporum is a P450-type enzyme (P450nor) that catalyzes the reduction of NO to nitrous oxide (N2O) in the global nitrogen cycle. In this enzymatic reaction, the heme-bound NO is activated by the direct hydride transfer from NADH to generate a short-lived intermediate ( I ), a key state to promote N-N bond formation and N-O bond cleavage. This study applied time-resolved (TR) techniques in conjunction with photolabile-caged NO to gain direct experimental results for the characterization of the coordination and electronic structures of I TR freeze-trap crystallography using an X-ray free electron laser (XFEL) reveals highly bent Fe-NO coordination in I , with an elongated Fe-NO bond length (Fe-NO = 1.91 Å, Fe-N-O = 138°) in the absence of NAD+ TR-infrared (IR) spectroscopy detects the formation of I with an N-O stretching frequency of 1,290 cm-1 upon hydride transfer from NADH to the Fe3+-NO enzyme via the dissociation of NAD+ from a transient state, with an N-O stretching of 1,330 cm-1 and a lifetime of ca. 16 ms. Quantum mechanics/molecular mechanics calculations, based on these crystallographic and IR spectroscopic results, demonstrate that the electronic structure of I is characterized by a singly protonated Fe3+-NHO•- radical. The current findings provide conclusive evidence for the N2O generation mechanism via a radical-radical coupling of the heme nitroxyl complex with the second NO molecule.

Obtaining Polyvinylpyrrolidone Fibers Using the Electroforming Method with the Inclusion of Microcrystalline High-Temperature Phosphates.

The results of the synthesis of microcrystalline calcium phosphates such as hydroxoapatite, pyrophosphate, and tricalcium phosphate are presented herein. The influence of the addition of polyvinylpyrrolidone (PVP) on the phase characteristics of the resulting high-temperature ceramic sample is considered. The X-ray results show that hydroxyapatite (HAp) consists of a Ca5(PO4)3(OH) phase, while the sample with the addition of polyvinylpyrrolidone contains ß-Ca3(PO4)2 (65.5%) and ß-Ca2P2O7 (34.5%) phases calcium phosphates (CPs). IR spectroscopy was used to characterize the compositions of the samples. An important characteristic of the obtained samples is the elemental Ca/P ratio, which was determined via energy-dispersive analysis. The data obtained are consistent with the composition of dental enamel apatites, namely, in the CPs (1.27) and HAp (1.40). SEM was used to study the morphology of the surfaces of hydroxyapatite particles. Polyvinylpyrrolidone polymer fibers were obtained using the electroforming method with the inclusion of CPs in the composition. The fibers were oriented randomly, and nanoscale hydroxyapatite particles were incorporated into the fiber structure. Solubility data of the HAp, CPs, and Fibers in a physiological solution at room temperature and human body temperature were obtained. The solubility of the resulting HAp turned out to be higher than the solubility of the CPs. In turn, the concentration of Ca2+ in a physiological solution of PVP composite fibers with the inclusion of CPs was lower than that in powdered CPs.

Polymer System Based on Polyethylene Glycol and TFE Telomers for Producing Films with Switchable Wettability.

Today a lot of attention is paid to the formation of thermosensitive systems for biomedical and industrial applications. The development of new methods for synthesis of such systems is a dynamically developing direction in chemistry and materials science. In this regard, this paper presents results of the studies of a new synthesized supramolecular polymer system based on polyethylene glycol and tetrafluoroethylene telomers. The films formed from the polymer substance have the property of switching wettability depending on temperature after heating activation. It has been established that the wettability changes at 60 °C. The contact angle of activated hydrophobic polymer film reaches 143°. Additionally, the system exhibits its properties regardless of the pH of the environment. Based on data obtained by the methods of infrared and x-ray photoelectron spectroscopy, differential thermal analysis and thermal analysis in conjunction with wettability and morphology, a model of the behavior of molecules in a polymer system was built that ensures switching of the hydrophilic/hydrophobic surface state. The resulting polymer system, as well as films based on it, can be used in targeted drug delivery, implantation surgery, as sensors, etc.

The Invisible Fraction within Melanin Capable of Absorbing UV Light and with Fluorescent Properties: Is It Lacking Consideration?

Expanding on earlier observations, we show that many melanin materials, in vitro synthesized from a wide range of precursors, can be fractionated into a dark-colored precipitate and a near-colorless, dispersible fraction. The dispersible fractions exhibited absorbance in the UVA and UVB range of the electromagnetic spectrum, but none in the visible range. In addition, fluorescent properties were associated with all dispersible fractions obtained. FT-IR spectroscopic analyses were performed to compare both types of fractions. Overall, it appears that some of the properties associated with melanin (UV absorbance, fluorescence) may not necessarily reside in the dark-colored portion of melanin, but in a colorless fraction of the material. It remains to be seen whether any of these in vitro observations have any relevance in vivo. However, we raise the possibility that the presence of a colorless fraction within melanin materials and their associated properties may have received inadequate attention. Given the important association between melanin, UV protection, and skin cancer, it is worthwhile to consider this additional aspect of melanin chemistry.

Infrared Spectroscopy of Neutral and Cationic Benzonitrile-Methanol Binary Clusters in Supersonic Jets.

The formation of nitrogen-containing organic interstellar molecules is of great importance to reveal chemical processes and the origin of life on Earth. Benzonitrile (BN) is one of the simplest nitrogen-containing aromatic molecules in the interstellar medium (ISM) that has been detected in recent years. Methanol (CH3OH) exists widely in interstellar space with high reactivity. Herein, we measured the infrared (IR) spectra of neutral and cationic BN-CH3OH clusters by vacuum ultraviolet (VUV) photoionization combined with time-of-flight mass spectrometry. Combining IR spectra with the density functional theory calculations, we reveal that the BN-CH3OH intends to form a cyclic H-bonded structure in neutral clusters. However, after the ionization of BN-CH3OH clusters, proton-shared N···H···O and N···H···C structures are confirmed to form between BN and CH3OH, with the minor coexistence of H-bond and O-π structures. The formation of the proton-shared structure expands our knowledge of the evolution of the life-related nitrogen-containing molecules in the universe and provides a possible pathway to the further study of biorelevant aromatic organic macromolecules.

Transformation of Silicate Ions into Silica under the Influence of Acid on the Structure of Serpentinite.

The process of transformation of the silicate components of the crystal lattice structure of chrysotile during its quantitative interaction with aqueous solutions containing various stoichiometrically required amounts of sulfuric acid (SRA H2SO4) calculated with respect to the magnesium content in the composition of chrysotile is investigated. It has been shown by IR spectroscopic, X-ray phase, thermal and chemical methods of investigation and analysis that, with quantitative interactions of chrysotile and sulfuric acid, first of all, the "brucite layer" of the molecular structural structure of chrysotile is exposed to acid at SRA H2SO4 = 0.1-0.3. As a result of ion exchange processes, acidic silanol (≡Si-O-H) or disilanol (=Si=(O-H)2) bonds are formed. These acid groups form one-dimensional silicate chains with transverse bridges (≡Si-O-Si≡), where the angles (Si-O-Si = 180 °C) straighten, which are recorded in the IR spectra in the region of characteristic absorption of 1220-1250 cm-1 silica. The association of the resulting acid groups into silicate chains, dimers, and trimers with transverse bridges, leads to the appearance of colloidal silica particles in the system, which cause some inhibition of the dissolution of layered magnesium hydrosilicate in sulfuric acid solutions containing H2SO4 ˃ 0.3 SRA.