Time-dependent vibrational spectral analysis of first principles trajectory of methylamine with wavelet transform

Rice Origin Tracing Technology Based on Fluorescence Spectroscopy and Stoichiometry

The origin of agricultural products is crucial to their quality and safety. This study explored the differences in chemical composition and structure of rice from different origins using fluorescence detection technology. These differences are mainly affected by climate, environment, geology and other factors. By identifying the fluorescence characteristic absorption peaks of the same rice seed varieties from different origins, and comparing them with known or standard samples, this study aims to authenticate rice, protect brands, and achieve traceability. The study selected the same variety of rice seed planted in different regions of Jilin Province in the same year as samples. Fluorescence spectroscopy was used to collect spectral data, which was preprocessed by normalization, smoothing, and wavelet transformation to remove noise, scattering, and burrs. The processed spectral data was used as input for the long short-term memory (LSTM) model. The study focused on the processing and analysis of rice spectra based on NZ-WT-processed data. To simplify the model, uninformative variable elimination (UVE) and successive projections algorithm (SPA) were used to screen the best wavelengths. These wavelengths were used as input for the support vector machine (SVM) prediction model to achieve efficient and accurate predictions. Within the fluorescence spectral range of 475-525 nm and 665-690 nm, absorption peaks of nicotinamide adenine dinucleotide (NADPH), riboflavin (B2), starch, and protein were observed. The origin tracing prediction model established using SVM exhibited stable performance with a classification accuracy of up to 99.5%.The experiment demonstrated that fluorescence spectroscopy technology has high discrimination accuracy in tracing the origin of rice, providing a new method for rapid identification of rice origin.

Direct Correlation between Short-Range Vibrational Spectral Diffusion and Localized Ion-Cage Dynamics of Water-in-Salt Electrolytes

The molecular dynamics simulations of a "water-in-salt" electrolyte, lithium bis(trifluoromethyl sulfonyl) imide (LiNTf₂), with a varying concentration range of 3 to 20 m were performed to establish a direct connection between a dynamic property like the ion-cage lifetime with the short-range vibrational stretching frequency shift of the used probe, HOD. The properties reported here are compared to that obtained from experiments performed at the same concentrations. The time-series wavelet transform was adopted as a preferable mathematical tool for calculating the instantaneous fluctuating frequencies of the probe O-D stretch mode and the concentration-dependent vibrational stretch spectral signature based on the variable functions associated with a particular chemical bond derived from classical molecular dynamics trajectories. The decay time constants of frequency fluctuations and the lifetime of the ion cage (τ_IC) were estimated as a function of salt concentration. Herein, we emphasize the correlation between the slowest time constant (τ₃) of the decay of O-D stretch frequency fluctuations and the timescales associated with the lifetime of ion cages (τ_IC). The results exhibit that the existing relationships were also concentration-dependent. Therefore, this study highlights the connection between the ionic motions that regulate the overall system dynamics with the short-range vibrational frequency shift of the used probe, which was used similar to experiments. It also provides an understanding of the interionic interactions and the dynamical and spectral properties of the electrolytic mixtures. We establish a direct correlation between short-range frequency profile and localized ion-cage lifetime, which can fill the gap of understanding between viscosity, vibrational frequency, and ion-cage dynamics of electrolytes.

Ionic Dynamics and Vibrational Spectral Diffusion of a Protic Alkylammonium Ionic Salt through Intrinsic Cationic N-H Vibrational Probe from FPMD Simulations

We employed density functional theory (DFT)-based molecular dynamics simulations to explore the structure, dynamics, and spectral properties of the protic ionic entity trimethylammonium chloride (TMACl). Structural investigations include calculating the site-site radial distribution functions (RDFs), the distribution of constituent cations and anions in three-dimensional space, and combined distribution functions of the hydrogen-bonded pair RDF versus angle, revealing the structural characteristics of the ionic solvation and the intermolecular interactions within ions. Further, we determined the instantaneous vibrational stretching frequencies of the intrinsic N-H stretch probe modes by applying the time-series wavelet method. The associated ionic dynamics within the protic ionic compound were investigated by calculating the time-evolution of the fluctuating frequencies and the frequency-time correlation functions (FFCFs). The time scale related to the local structural relaxation process and the average hydrogen bond lifetime, ion cage dynamics, and mean squared displacement were investigated. The faster decay component of the FFCFs, depicting the intermolecular motion of intact hydrogen bonds in TMACl, is 0.07 ps for the Perdew-Burke-Ernzerhof (PBE)-based simulation and 0.06 ps for the PBE-D2 representation. The slower time scale of the longer picosecond decay time component of PBE and PBE-D2 representations are 3.13 and 2.87 ps, respectively. These picosecond time scales represent more significant fluctuations of the hydrogen-bonding partners in the ionic entity and hydrogen-bond jump events accompanied by large angular jumps. The longest picosecond time scales represent structural relaxation, including large angular jumps and ion-pair dynamics. Also, ion cage lifetimes correlate with the slowest time scale of the associated dynamics of vibrational spectral diffusion despite the type of DFT functional. This study benchmarks DFT treatments of the exchange-correlation functional with and without the van der Waals (vdW) dispersion correction scheme. The inclusion of vdW interactions to the PBE functional represents a less structured state of the ionic entity and faster dynamics of the molecular motions relative to the one predicted by the PBE system. All the results illustrate the necessity of accurately describing the Coulomb interactions, vdW dispersive interactive forces, and localized hydrogen bonds required to sustain the energetic balance in this ionic salt.

Dynamics of Ionic Liquid through Intrinsic Vibrational Probes Using the Dispersion-Corrected DFT Functionals

First principles molecular dynamics simulations have been utilized to study the spectral properties of the protic ionic liquid, methylammonium formate (MAF). All simulations were performed using density functional theory (DFT) and various van der Waals-corrected exchange-correlation functionals. We calculated the vibrational stretch frequency distributions, determined the time-frequency correlations of the intrinsic vibrational probes, the N-H and C-O modes in MAF, and the frequency-structure correlations. We also estimated the average hydrogen-bond lifetimes and orientation dynamics to capture the ultrafast spectral response. The spectroscopic signature of the N-H stretching vibrations using the Becke-Lee-Yang-Parr (BLYP) and Perdew-Burke-Ernzerhof (PBE) functionals displays a spectral shift in the lower frequency side, suggesting stronger hydrogen-bonding interactions represented by the gradient approximation functionals than the van der Waals (vdW)-corrected simulations. The carboxylate frequency profiles with the dispersion-corrected representations are almost similar without a significant difference in the normalized distributions. Besides, the COO stretching frequencies at the peak maxima positions of the PBE functionals exhibit a lesser deviation from the experimental data. Spectral diffusion dynamics of the intrinsic vibrational probes on the cationic and anionic sites of the ionic liquid proceed through a short time relaxation of the intact hydrogen bonds followed by an intermediate time constant and a longer time decay indicating the switchover of hydrogen bonds. Dispersion-corrected atom-centered one-electron potential (DCACP) correction added to the BLYP system slows down the picosecond time scales of frequency correlation and the time constants of rotational motion, lengthening the overall system dynamics. The observed trends in the time-dependent decays of frequency fluctuations and the orientation autocorrelation functions correlate with the structural interactions in liquid MAF and hydrogen-bond dynamics. In this study, we examine the predictions made by different density functional treatments comparing the results of the uncorrected BLYP and PBE representations with the semiempirical vdW methods of Grimme and matching our calculated data with the experimental observations.

Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent's effect on the vibrational frequency.

Conformation-induced vibrational spectral dynamics of hydrogen peroxide and vicinal water molecules

We studied the conformation-induced spectral response of water molecules due to site-specific structural alterations of solvated hydrogen peroxide (H₂O₂) employing DFT-based first principles molecular dynamics (FPMD) simulations. Wavelet transform was used to determine the time-dependent frequencies of the hydroxyls of water molecules and the O-H stretch modes of H₂O₂. Shifts in the vibrational frequency of the hydrogen-bonded hydroxyls inside the solvation shell of H₂O₂ support multiple distinctive hydrogen bonding environments. This paper classifies two distinct hydrogen bond types inside the O-O_W solvation shell of H₂O₂, and the dynamical calculations provide a quantitative estimation of the relative hydrogen bond strength. We ascertain the reason for not observing the escape of water molecules from the hydrogen peroxide hydration shell, unlike the solvation shell of ionic solutions and neutral solutes. Besides, we provide a comprehensive analysis of the spectral shifts in the normalized frequency distribution, the time-dependent decay of frequency-frequency correlation functions, and the hydrogen bond length scale fluctuations. We also quantify the relative contribution of the cisoid and transoid conformers affecting the vibrational spectral signature of the vicinal water molecules. While the transoid conformers promote the hydrogen bonding interactions through the oxygen site (OH_W), the cisoid conformers facilitate hydrogen peroxide-water hydrogen bond formation through the hydrogen site (HO_W). These non-identical hydrogen bond associations stabilize hydrogen peroxide in water.

Ab initio molecular dynamics study of sodium NMR chemical shifts in the methylamine solution of [Na+ [2.2.2]cryptand Na-]

The sodium anion (Na-) was once thought to behave like a 'genuine' anion, with both the [Ne] core and the 3s valence shell interacting very weakly with their environments. In the present work, following a recent study of the surprisingly small quadrupolar line widths of Na-, NMR shielding calculations were carried out for the Na-/Na+ [2.2.2]cryptand system solvated in methylamine, based on ab initio molecular dynamics simulations, followed by detailed analyses of the shielding constants. The results confirm that Na- does not act like a quasi-free ion that interacts only weakly with its surroundings. Rather, the filled 3s shell of Na- interacts strongly with its chemical environment, but only weakly with the ion's own core and the nucleus, and it isolates the core from the chemical environment. As a consequence, the Na- ion appears in NMR experiments like a free ion.

The Sodium Anion Is Strongly Perturbed in the Condensed Phase Even Though It Appears Like a Free Ion in Nuclear Magnetic Resonance Experiments

Solvated sodium anions (Na^-) were thought to behave essentially like isolated gas-phase ions that interact only weakly with their environments. For example, ²³Na NMR signals for solvated Na^- are very sharp, despite the potential for strong quadrupolar broadening. The sharp NMR signals appear to indicate a nearly spherical electron density of the ion. For the present study, ab initio molecular dynamics simulations and quadrupolar relaxation rate calculations were carried out for the Na^-/Na⁺ [2.2.2]cryptand system solvated in methylamine, followed by detailed analyses of the electric field gradient at the sodium nuclei. It is found that Na^- does not behave like a quasi-free ion interacting only weakly with its environment. Rather, the filled 3s shell of Na^- interacts weakly with the ion's own core and the nucleus, causing Na^- to appear in NMR experiments like a free ion.

Ab initio metadynamics calculations of dimethylamine for probing pKb variations in bulk vs. surface environments

Free energy landscape obtained from ab initio metadynamics calculations for dimethylamine protonation at the air–water interface.

Heterogeneous Occupancy and Vibrational Dynamics of Spatially Patterned Water Molecules

We performed first-principles molecular dynamics simulations of relatively dilute aqueous solutions of sulfate and thiosulfate dianions to analyze the structure, dynamics, and vibrational spectral properties of water molecules around the solute, especially the spatially patterned solvent molecules in the first solvation layer and the extended layers. This study also involves the investigation of dynamics of dangling OH groups in these layers and their role in patterning the water molecules around the dianions. Structural evaluation of the systems is carried out by radial distribution functions, number integrals, and spatial distribution functions. The lifetime of dangling OH groups inside the solvation shell is compared more to that of the bulk. By constructing the O-H groups in three ensembles (S1, S2, and S3) around the anion, we show that the frequency distribution of OH modes in the S1 ensemble show red-shifting for both sulfate and thiosulfate. The O-H groups in the S2 ensemble of the sulfate-water system show red-shifting by 10 cm^-1, while in the case of thiosulfate-water, these O-H groups show blue-shifting by 8 cm^-1. The water molecules in S1 and S2 subensembles have slower dynamics compared to those in the bulk (S3). The dynamics of various kinds of hydrogen bonds were characterized by hydrogen bond population correlation functions. The spectral diffusion of solvation shell O-H modes was performed through a frequency-time correlation function. We find a significant amount of orientational retardation of water molecules in the S1 layer and moderate retardation in the S2 layer as compared to that in the bulk, S3 layer. All these findings, the red shift of the OH stretching frequency in S1 and S2 layers, slowing down of the orientational dynamics of OH vectors in S1 and S2 layers, and less diffusivity of water in S1 and S2 layers, show the long-range kosmotropic effect of multivalent sulfate and thiosulfate oxyanions. Due to the long-range effect, heterogeneous occupancy of water molecules is observed, and the water molecules are found to arrange in a patterned manner in the vicinity of anions with varied local density.

Vibration Spectral Dynamics of Weakly Coordinating Water Molecules near an Anion: FPMD Simulations of an Aqueous Solution of Tetrafluoroborate

The extent to which the ions affect the nearby water molecules will decide the structure-making or breaking nature of those ions in aqueous solutions. The effects of a weakly coordinating anion on the structure, dynamics, and vibrational properties of water molecules are not so significant as compared to an anion capable of making strong ion-water hydrogen bonds. The present work deals with the first-principles molecular dynamics study of an aqueous solution of such a weakly coordinating anion, tetrafluoroborate (BF₄^-), using dispersion-corrected DFT-based first-principles molecular dynamics (FPMD) simulations. Various structural, dynamical, and spectral properties, such as radial distribution functions (RDFs), rotational dynamics, vibrational density of states (VDOS), hydrogen bond as well as dangling OH autocorrelation functions, and residence dynamics, were calculated to investigate the effects of the anion on nearby water molecules. The process of spectral diffusion was assessed through a time series wavelet transformation of trajectories obtained from FPMD simulations. The first ion-water solvation shell extends up to 5.5 Å, containing around 20 water molecules. The lifetime of the ion-water hydrogen bond is found to be 1.19 ps, whereas the water-water hydrogen bond lifetime is found to be 1.13 ps. Inside the solvation shell, the persistence time of dangling OH chromophores and the average frequency of OH modes inside the solvation shell are found to be more compared to bulk. Three time scales are found for solvation shell OH modes from the frequency-frequency correlation function. A very short time scale is found for the intact ion-water interaction; the short time scale is for the ion-water hydrogen bond, and the long time scale is for escape dynamics of water molecules from the ion solvation shell. From the mean squared displacement, it is found that solvation water molecules diffuse slower than the bulk. However, solvation shell water molecules show faster relaxation from the analysis of rotational anisotropy. Within the longer time scale of spectral diffusion, this process (which is related to various dynamics of the molecules) is not yet complete, as compared to fast anisotropic decay. This fact is similar to the experimental finding of spectral diffusion and anisotropy time scales in the aqueous solution of borohydride anion. The calculated results are also compared with available experimental data wherever possible.