Experimental Spectra Research Articles

Leveraging infrared spectroscopy for automated structure elucidation.

The application of machine learning models in chemistry has made remarkable strides in recent years. While analytical chemistry has received considerable interest from machine learning practitioners, its adoption into everyday use remains limited. Among the available analytical methods, Infrared (IR) spectroscopy stands out in terms of affordability, simplicity, and accessibility. However, its use has been limited to the identification of a selected few functional groups, as most peaks lie beyond human interpretation. We present a transformer model that enables chemists to leverage the complete information contained within an IR spectrum to directly predict the molecular structure. To cover a large chemical space, we pretrain the model using 634,585 simulated IR spectra and fine-tune it on 3,453 experimental spectra. Our approach achieves a top-1 accuracy of 44.4% and top-10 accuracy of 69.8% on compounds containing 6 to 13 heavy atoms. When solely predicting scaffolds, the model accurately predicts the top-1 scaffold in 84.5% and among the top-10 in 93.0% of cases.

Understanding the Mid-Infrared Spectra of Protic Ionic Liquids by Density Functional Theory.

Protic ionic liquids (PILs) are promising candidates as electrolytes for proton exchange polymer membrane fuel cells. In order to optimize their properties, a detailed understanding of the molecular interactions within the bulk and at the electrode-electrolyte interface is needed, which can be obtained by infrared spectra. A prerequisite for extracting information on the molecular structure and inter- or intramolecular interactions from an experimental spectrum is a reasonable interpretation of the observed spectral features. Here, we employed density functional theory to understand the vibration modes of PILs composed of ammonium cations and different counteranions. Different from the previous calculation methods performed on small cluster model systems consisting of isolated species, a periodically repeated system of four ion pairs was used in order to approximate the bulk liquid environment. The computed frequencies and IR intensity match well with the corresponding experimental spectra, allowing for its proper interpretation, especially the characteristic features of the interionic interaction. The presented approach enables accurate computation of a variety of ionic liquid systems in a highly efficient way.

Molecular modeling analyses of functionalized cellulose.

Functionalization of cellulose with nanomaterials and functional groups is essential for enhancing its properties for specific applications, such as flexible sensors and printed electronics. This study employs Hartree Fock (HF) and Density Functional Theory (DFT) calculations to investigate the vibrational spectra of cellulose, identifying DFT: B3LYP/3-21g** as the optimal model aligning with experimental spectra. Using this model, we examined the impact of functionalizing cellulose with various groups (OH, NH2, COOH, CH3, CHO, CN, SH) and graphene oxide (GO) on its electronic properties. The results indicate that cellulose functionalized with GO (Cellulose-GO) has the lowest bandgap energy (0.1687eV), and improvements in reactivity, stability, and electronic properties were confirmed through Molecular Electrostatic Potential (MESP) and Total Dipole Moment (TDM) analyses. The spectrum of Density of States (DOS) for the cellulose functionalized with different groups shows several peaks, indicating various energy levels where electronic states are concentrated. The Projected Density of States (PDOS) analysis reveals how different functional groups affect the electronic structure of cellulose. Moreover, the (Cellulose-GO) composite was characterized using an Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectrometer, revealing interaction through the OH group of CH2OH, as indicated by a new band at 1710cm-1, consistent with theoretical predictions. Overall, this study demonstrates that functionalization with GO enhances cellulose's responsiveness, degradation, and electrical properties, making it suitable for applications in flexible electronic devices and protective barriers against corrosion.

Investigating the effect of non-resonant background variation on the CARS data analysis of bacteria samples and classification using machine learning

Non-resonant background (NRB) plays a significant role in coherent anti-Stokes Raman scattering (CARS) spectroscopic applications. All the recent works primarily focused on removing the NRB using different deep learning methods, and only one study explored the effect of NRB. Hence, in this work, we systematically investigated the impact of NRB variation on Raman signal retrieval. The NRB is simulated as a linear function with different strengths relative to the resonant Raman signal, and the variance also changes for each NRB strength. The resonant part of nonlinear susceptibility is extracted from real experimental Raman data; hence, the simulated CARS data better approximate the experimental CARS spectra. Then, the corresponding Raman signal is retrieved by four different methods: maximum entropy method (MEM), Kramers-Kronig (KK), convolutional neural network (CNN), and long short-term memory (LSTM) network. Pearson correlation measurements and principal component analysis combined with linear discriminant analysis modeling revealed that MEM and KK methods have an edge over LSTM and CNN for higher NRB strengths. It is also demonstrated that normalizing the input data favors LSTM and CNN predictions. In contrast, background removal from the predictions significantly influenced Pearson correlation but not the classification accuracies for MEM and KK. Further, the LSTM performance is found to be limited and can only be applied for low NRB strengths. This comprehensive study has the potential to impact the CARS spectroscopy and microscopy applications in different areas.

Anti-inflammatory diterpenoids from the brown alga Dictyota coriacea.

A new xenicane diterpene named 4α-acetoxyisodictyohemiacetal (1) was isolated from the brown alga Dictyota coriacea, along with 11 known diterpenoids. The structure of 1 was established by spectroscopic analyses, and its absolute configuration was determined by comparing the experimental and theoretical electronic circular dichroism (ECD) spectra. Two dictyodiacetal diastereomers (5 and 6) were isolated and the full NMR assignments were performed. The anti-inflammatory activities of the isolated compounds were evaluated using the lipopolysaccharide-stimulated mouse macrophage cell line, RAW264. The hemiacetal-containing xenicanes and dictyol-type diterpene inhibited not only the production of nitric oxide, but also the expression of inducible nitric oxide synthase, interleukin-6, and cyclooxygenase-2 mRNA in RAW264 cells. This study demonstrated that diterpenes from Dictyota coriacea may be useful as natural anti-inflammatory agents.

Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes.

Vibrational non-Condon effects, which describe how molecular vibrational transitions are influenced by a system's rotational and translational degrees of freedom, are often overlooked in spectroscopy studies of biological macromolecules. In this work, we explore these effects in the modeling of infrared (IR) spectra for nucleic acids in the 1600-1800 cm-1 region. Through electronic structure calculations, we reveal that the transition dipole moments of the C═O and C═C stretching modes in nucleobases are highly sensitive to solvation, hydrogen bonding, and base stacking conditions. To incorporate vibrational non-Condon effects into spectroscopy modeling, we use local electric fields on chromophore atoms as collective coordinates and leverage experimental IR spectra of oligonucleotides to develop deep neural network-based transition dipole strength (TDS) maps for the C═O and C═C chromophores. By integrating molecular dynamics simulations with a mixed quantum/classical treatment of the line shape theory, we apply the TDS maps to calculate the IR spectra of nucleoside 5'-monophosphates, DNA double helices and yeast phenylalanine tRNA. The resulting theoretical spectra show quantitative agreement with experimental measurements. While the predictions for nucleoside 5'-monophosphates are comparable to baseline performance, the TDS maps yield significantly improved IR peak intensities across all oligonucleotides. This theoretical framework effectively bridges atomistic simulations and IR spectroscopy experiments, offering molecular insights into how vibrational non-Condon effects impact the observed spectral features.

Temperature Controlled Decay and Pendulum Dynamics of Green Fluorescent Protein (GFP) Chromophore.

The excited-state dynamics of the GFP chromophore, HBDI- (anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone), were investigated through a combination of theoretical nonadiabatic molecular dynamics (NAMD) simulations and femtosecond transient absorption spectroscopy (fs-TA). The NAMD simulations revealed that the primary dynamics in excited states involve the formation of a P-twisted intermediate (S1min,P), which undergoes pendulum-like oscillations with respect to ϕ = 90°. This motion serves as a reservoir for the excited-state population and the primary source of fluorescence. Rather than a direct channel from the major S1min,P, a coordinated pathway of S1min,P → S1min → S1min,I → S0 is responsible for the decay to the ground state, emphasizing the importance of planar intermediate (S1min) formation. The experimental fs-TA spectra confirmed these dynamics, revealing three distinct time scales (340-470 fs, 1.4 ps, and 8.3 ps), corresponding to the formation of S1min,P and its decay governed by the coordinated pathway. At low temperatures, the coordinated decay pathway is suppressed, leading to prolonged fluorescence lifetimes, consistent with low-temperature experimental results. This study presents a new model for the excited-state dynamics of GFP chromophore, suggesting that pendulum motion and the coordinated decay pathway play a crucial role in regulating fluorescence intensity.

π+π− Coulomb interaction study and its use in data processing

In this work, the Coulomb effects (Coulomb correlations) in π+π− pairs produced in p+Ni collisions at 24 GeV/c, are studied using experimental π+π− pair distributions in Q, the relative momentum in the pair center-of-mass system (c.m.s.), and its projections QL (longitudinal component) and Qt (transverse component) relative to the pair direction in the laboratory system (LS). The major part of the pion pairs (“Coulomb pairs”) is produced in the decay of ρ, ω and Δ resonances and other short-lived sources. In these pairs, the significant Coulomb interaction occurs at small Q, dominating the π+π− interaction in the final state. The minor part of the pairs (“non-Coulomb pairs”) is produced if one or both pions arose from long-lived sources like η,η′ or from different interactions. In this case, the final state interaction is practically absent. The Q, QL, and Qt distributions of the Coulomb pairs in the c.m.s. have been simulated assuming they are described by the phase space modified by the known point-like Coulomb correlation function AC(Q), corrected for small effects due to the nonpointlike pair production and the strong two-pion interaction. The same distributions of non-Coulomb pairs have been simulated according to the phase space, but without AC(Q). In all Qt intervals, the experimental QL spectrum shows a peak around QL=0 caused by the Coulomb final state interaction. The full width at half maximum increases with Qt from 3 MeV/c for 0<Qt<0.25 MeV/c to 11 MeV/c for 4.0<Qt<5.0 MeV/c. The experimental QL distributions have been fitted with two free parameters: the fraction of Coulomb pairs and the normalization constant. The precision of the description of these distributions is better than 2% in Qt intervals 2–3, 3–4, and 4–5 MeV/c and better than 0.5% in the total Qt interval 0–5 MeV/c. It is shown that the number of Coulomb pairs in all Qt intervals, including the small Qt (small opening angles θ in the LS) is calculated with theoretical precision better than 2%. The comparison of the simulated and experimental numbers of Coulomb pairs at small Qt allows us to check and correct the detection efficiency for the pairs with small θ (0.06 mrad and smaller). It is shown that Coulomb pairs can be used as a new physical tool to check and correct the quality of the simulated events. The special property of the Coulomb pairs is the possibility of checking and correcting the detection efficiency, especially for the pairs with small opening angles. Published by the American Physical Society 2024

Rapid Raman spectroscopy analysis assisted with machine learning: a case study on Radix Bupleuri.

Radix Bupleuri has been widely used for its plentiful pharmacological effects. But it is hard to evaluate their safety and efficacy because the concentrations of components are tightly affected by the surrounding environment. Thus, Radix Bupleuri samples from different regions and varieties were collected. Based on the experimental and computational Raman spectrum, machine learning is emphasized for certain obscured characteristics; for example, linear discriminant analysis (LDA), support vector machine (SVM), eXtreme gradient boosting (XGBoost) and light gradient boosting machine (LightGBM). After dimension reduction by LDA, models of SVM, XGBoost and LightGBM were trained for classification and regression prediction of Bupleurum production regions. Support vector classifiers achieved the best accuracy of 98% and an F1 score above 0.96 on the test set. Support vector regression has a good fitting performance with an R2 score above 0.90 and a relatively low mean square error. However, complex models were prone to overfitting, resulting in poor generalization ability. Among these machine learning models, the typical LDA-SVM models, consistent with the high-performance liquid chromatography results, demonstrate great performance and stability. We envision that this rapid classification and regression technique can be extended to predictions for other herbs. © 2024 Society of Chemical Industry.

Synthesis, Chiroptical Properties, and Absolute Configuration Determination of Phenyl‐4‐pyridyl‐2,5‐dipyrimidinylmethane

Phenyl‐4‐pyridyl‐2,5‐dipyrimidinylmethane (1) has been synthesized in five steps from 5‐methylpyrimidine. The structural feature of 1 is the symmetry elements with respect to the 180º rotation of the aryl group along the central C‐C bonds. Due to this structural feature, the compound 1 is expected the good crystallinity despite of the asymmetric molecular structure. The optical resolution of 1 was achieved by high performance liquid chromatography using chiral stationary phase (chiral HPLC). The circular dichroism (CD) spectra of the two fractions showed opposite signs. As expected, the X‐ray crystallographic analysis was successfully performed for both the racemic and enantiomerically pure crystals of compound 1, with the nitrogen atoms being unambiguously assigned in both cases. It was concluded the first‐eluted fraction in chiral HPLC was determined to be S configuration both by the CD calculation for reproducing the experimental CD spectrum and by the anomalous diffraction of X‐ray crystallographic analysis of enantiomerically pure 1.

Revisiting the global minimum of Au10 clusters.

This study employs high-level quantum chemical calculations to determine the global minimum structure of Au10 clusters definitively. Contrary to previous reports, coupled-cluster singles and doubles with perturbative triples [CCSD(T)] calculations with sizable quadruple-ζ basis sets incorporating the spin-orbit (SO) effect reveal that the planar 10.b structure is the true global minimum for Au10, not the three-dimensional 10.a structure. Two-component spin-orbit density functional theory calculations demonstrate that the SO effect is minimal for most Au10 isomers, except for the 10.f structure. A straightforward diagnostic tool is proposed for identifying Au cluster structures with strong spin-orbit coupling based on 6p orbital occupation. The calculated IR spectra based on Boltzmann averaging the six Au10 isomers show good agreement with recent experimental spectra although minor discrepancies are noted potentially due to interactions with Kr. The results suggest that the transition point to non-planar global minimum structures for Au clusters lies beyond Au10 but is nearby.

A framework to model charge sharing and pulse pileup for virtual imaging trials of photon-counting CT

Objective.This study describes the development, validation, and integration of a detector response model that accounts for the combined effects of x-ray crosstalk, charge sharing, and pulse pileup in photon-counting detectors.Approach.The x-ray photon transport was simulated using Geant4, followed by analytical charge sharing simulation in MATLAB. The analytical simulation models charge clouds with Gaussian-distributed charge densities, which are projected on a 3×3 pixel neighborhood of interaction location to compute detected counts. For pulse pileup, a prior analytical method for redistribution of energy-binned counts was implemented for delta pulses. The x-ray photon transport and charge sharing components were validated using experimental data acquired on the CdTe-based Pixirad-1/Pixie-III detector using monoenergetic beams at 26, 33, 37, and 50 keV. The pulse pileup implementation was verified with a comparable Monte Carlo simulation. The model output without pulse pileup was used to generate spatio-energetic response matrices for efficient simulation of scanner-specific photon-counting CT (PCCT) images with DukeSim, with pulse pileup modeled as a post-processing step on simulated projections. For analysis, images for the Gammex multi-energy phantom and the XCAT chest phantom were simulated at 120 kV, both with and without pulse pileup for a range of doses (27-1344 mAs). The XCAT images were evaluated qualitatively at 120 mAs, while images for the Gammex phantom were evaluated quantitatively for all doses using measurements of attenuation coefficients and Calcium concentrations.Main results.Reasonable agreement was observed between simulated and experimental spectra with Mean Absolute Percentage Error Values (MAPE) between 10%and 31%across all incident energies and detector modes. The increased pulse pileup from increased dose affected attenuation coefficients and calcium concentrations, with an effect on calcium quantification as high as MAPE of 28%.Significance.The presented approach demonstrates the viability of the model for enabling VITs to assess and optimize the clinical performance of PCCT.

Molecular properties of a triazole–Ce(III) complex with antioxidant activity: structure, spectroscopy, and relationships with related derivatives. Influence of the ligands in the complex

A novel Ce(III) complex with the triazole ligand 2b, which presents four H-bonded sites with amino acids of the MMP-2 receptor, was synthesized. The experimental IR and Raman spectra of this Ce(III) complex were well-interpreted based on their comparison to the theoretical scaled spectra using the scaling equations determined by two procedures and four density functional theory (DFT) levels. Therefore, the structure predicted for the synthesized Ce(III) complex was clearly characterized and confirmed. The potential antioxidant action of this complex was compared with the analogous La(III) complex, and it was found that the coordination of ligand 2b with Ce(III) improves the ligand’s ability to participate in single-electron transfer (SET), as observed in the ABTS·+ assay, and this complex seems to scavenge the stable radical much more actively compared to its La(III) counterpart. Additionally, interactions with potassium superoxide and sodium hypochlorite indicate a high pro-oxidant behavior of the complex. The effects of different ligands on the geometric parameters, atomic charges, and molecular properties of the Ce(III) complex were analyzed at four DFT levels, and several relationships were clearly established. These relationships can facilitate the selection of new ligands with improved properties in the design of novel lanthanide–triazole carboxylate complexes with promising biological activity. The ligand size increase in the complexes facilitates the electronic transfer of negative charge, and the low HOMO (highest occupied molecular orbital)–LUMO (lowest unoccupied molecular orbital) energy gap indicates a large reactivity and low energy for their excitation.

Glycosparvine A, a new indole alkaloid from the leaves of Glycosmis parviflora

In the course of our ongoing search for biologically active compounds from medicinal plant, the ethyl acetate extract from the leaves of Glycosmis parviflora (Rutaceae) was investigated. Six compounds including a new indole alkaloid, glycosparvine A (1), and five previously known metabolites (2–6) were identified. The structure of the new compound (1) was unambiguously elucidated by spectroscopic analyses, including 1D/2D NMR spectroscopy and HRESIMS. The absolute configuration of 1 was assigned by comparing its experimental ECD spectra with those reported for similar compound in the literature. Compounds 3 and 6 exhibited moderate inhibitory effects against acetylcholinesterase (AChE) with IC50 values of 35.1 and 2.8 mM, respectively.

An Investigation of the Structures of [(Glycine)(1-Methyluracil)]M+ Complexes (M = H, Li, Na, K) in the Gas Phase by IRMPD Spectroscopy and Theoretical Methods.

The presence of ions in the complexation of molecules can profoundly affect the structure, resulting in changes to functionality and stability. These non-covalent interactions drive many biological processes both necessary and inimical and require extensive research to understand and predict their effects. Protonated and alkali metalated complexes of glycine (Gly) and 1-methyluracil (1-mUra) were studied using infrared multiphoton dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations. The experimental and simulated vibrational spectra were compared to help elucidate the structure of each complex. The lowest energy structure for [(Gly)(1-mUra)]H+ consists of amine protonated Gly bound to O4 of canonical 1-mUra through a single ionic hydrogen bond with another, intraglycine ionic hydrogen bond between the protonated amine group and the carbonyl oxygen. For [(Gly)(1-mUra)]Li+, [(Gly)(1-mUra)]Na+ and [(Gly)(1-mUra)]K+, the experimental spectra are most consistent with the metal cations binding in a trigonal planar geometry with 1-mUra bound to the metal cation via the O4 carbonyl. In [(Gly)(1-mUra)]Li+ and [(Gly)(1-mUra)]Na+, the metal cation is bound to canonical Gly via the carbonyl oxygen and amine nitrogen, but in [(Gly)(1-mUra)]K+, Gly is bound through both oxygens and contains an intraglycine hydrogen bond from the hydroxyl to the amine nitrogen.

Optical and EPR study of Mn4+ ions in different crystal environments in Mn, Li co-doped MgO

The influence of Li ion on the symmetry of Mn4+ center and its photoluminescence (PL) in MgO:0,01%Mn, 3% Li ceramics is studied by the X-ray diffraction, electron paramagnetic resonance (EPR), PL and optical absorption methods. It is shown that Li co-doping stimulates conversion of Mn2+ on Mg site into Mn4+ and can decrease symmetry of Mn4+ in a case of their specific close arrangement in the crystal lattice. Two kinds of Mn4+ centers are identified in the EPR and PL spectra: cubic Mn4+ and tetragonal complex Mn4+-Li+. The parameters of corresponding EPR centers are estimated from the experimental spectra (gcub=1.994, |A|cub=70.9x104 cm-1; g1tetr=g2tetr=1.994, g3tetr=1.993, |A|tetr=71x104 cm-1, |D|tetr=220x104 cm-1). The PL lines observed in the low temperature PL spectra are assigned to the specific Mn4+ related centers by using a complementary study of PL excitation spectra and temperature dependent PL spectra. The lines at 654 nm and 671 nm are ascribed to R-line of Mn4+ in a site of cubic symmetry and its phonon overtone, correspondingly, as well as the lines at 666 nm and 681 nm are attributed to R2 line of Mn4+ in site with tetragonal symmetry and to its phonon overtone, correspondingly. It is shown that in Mn doped MgO ceramics made without intentional Li co-doping, the cubic Mn4+ center can be present and contribute to the PL spectra.

Analytical and numerical models for impedance of a button SOFC anode

We report a physics–based model for the impedance of a button–type anode–supported SOFC. The model includes ion and electron charge conservation equations and a Fick’s diffusion transport equation for hydrogen in the anode support layer. In the limit of small overpotentials, an analytical solution for the anode impedance is derived. For typical SOFC anode parameters, this solution is valid from open–circuit voltage (OCV) up to the cell current density of about 5 mA cm−2. Fast least–squares fitting of the model impedance to an experimental spectrum measured at OCV is demonstrated and the resulting fitting parameters are compared with literature data. A high–current numerical version of the model is also suitable for fast fitting of experimental impedance spectra.

Mixed (NH4)2Mn0.47Cu0.53(SO4)2(H2O)6 Tutton salt: A novel optical material for solar-blind technology

In this paper, a novel mixed Tutton salt (NH4)2Mn0.47Cu0.53(SO4)2(H2O)6 obtained in single crystal form is described. Their structural, thermal, electrical, and spectroscopic properties have been examined, and their possible uses are discussed. The salt crystallizes in a monoclinic symmetry (P21/c) and exhibits thermal stability between 300-333 K. Above this temperature, the crystal undergoes phase changes associated with dehydration and crystallization processes. 231 optical phonons distributed between 50 and 4000 cm–1, calculated through density functional perturbation theory, were used to accurately assign vibrational modes in experimental FT-IR and Raman spectra. Additional computational studies using Hirshfeld surfaces have revealed that H···O/O···H and H···H intermolecular contacts are crucial interactions for stabilizing the crystal lattice. Electrical characteristics (resistivity = 1160 MΩ·cm; capacitance = 3.6 pF) and optical data (bandgap = 4.27 eV) depict a typical behavior of nonpolar dielectric materials. UV-Vis-NIR transmittance spectrum has shown deep light blocking in the UV-C and Vis/NIR spectral regions and high transmittance levels (reaching 98.5%) in the UV-B/-A/Vis range. The photoresponse findings point out that (NH4)2Mn0.47Cu0.53(SO4)2(H2O)6 is a promising light-absorbing material for solar-blind photodetection devices operating in the 200-280 nm interval. The crystal as a bandpass filter (280-615 nm) or a cut-off filter (615-1000 nm) are also excellent prospects for application.

Novel fast full-wavefield modeling of air-coupled surface waves and its implications for non-contact pavement testing

We present a novel approach for deriving and modeling air-coupled surface waves with applications in non-contact non-destructive testing (NDT). It is based on the fast Fourier-Bessel series system in conjunction with the unconditionally stable dual-variable and position matrix method. Parametric studies, including sensitivity analysis, are conducted to assess the feasibility of using non-contact air-coupled measurements for pavement testing, focusing on Green's functions, time-domain waveforms, and experimental frequency-velocity spectra (FVS, i.e., the estimated Green's functions from acquired truncated wavefield). The predicted experimental FVS presented in this study are synthetic dispersion images, which are distinguished from the measured experimental FVS (i.e., measured dispersion images from multichannel analysis of surface wave (MASW) test). With the derived complete solution of air-coupled dynamic responses, we find that: (1) Striking similarities between the theoretical Green's functions of vertical displacement (on the pavement surface) and pressure (in the air), as well as in their corresponding experimental FVS. (2) The proposed accurate and efficient full-wave modeling of air-coupled surface waves avoids the need for good contact between geophones/accelerometers and pavement surface. This facilitates direct inversion of shear wave velocity profiles by fitting the predicted experimental FVS to the measured one. (3) Sensitivity analysis demonstrates no significant loss of information in the pressure measured in the air, supporting the feasibility of using non-contact measurement for non-destructive testing. These results suggest that non-contact air-coupled measurements hold great promise as a viable alternative to contact measurements in non-destructive testing.

Structure Determination of Zinc and Cadmium Dication Complexes with Intact and Deprotonated Histidyl Glycine and Glycyl Histidine Dipeptides.

Metalated intact and deprotonated histidyl glycine and glycyl histidine dipeptides were investigated in the gas phase by using infrared multiple photon dissociation (IRMPD) spectroscopy with light from a free-electron laser (FEL). The dipeptides M2+(GlyHis), M2+(HisGly), [M(GlyHis-H)]+, and [M(HisGly-H)]+, where M = Zn and Cd, were probed to elucidate how the His position along the peptide chain and ligand charge state might influence the structures observed in the gas phase. Simulated annealing calculations were performed to determine energetically low-lying conformers and isomers of these structures. Quantum chemical calculations were used to optimize the structures at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for zinc and cadmium complexes, respectively. IRMPD and calculated linear absorption spectra were compared to evaluate which structures are present. Relative energies of the various species were evaluated using single-point energy calculations for low-lying structures at the B3LYP, B3LYP-GD3BJ, ωB97XD, and MP2(full) levels using the 6-311+G(2d,2p) and def2-TZVPP basis sets. For all species, structures for both metals mirror each other, and those that reproduce the experimental spectrum were determined to be iminol structures for the intact ligands or iminol-like structures for the deprotonated ligands. Additionally, when the spectra of the deprotonated dipeptides are compared to the intact dipeptides, the change in the spectra is correlated to the group that is deprotonated.