Enhanced vibrational solvatochromism and spectral diffusion by electron rich substituents on small molecule silanes

Machine Learning Approach Based on a Range-Corrected Deep Potential Model for Efficient Vibrational Frequency Computation

As an ensemble average result, vibrational spectrum simulation can be time-consuming with high accuracy methods. We present a machine learning approach based on the range-corrected deep potential (DPRc) model to improve the computing efficiency. The DPRc method divides the system into "probe region" and "solvent region"; "solvent-solvent" interactions are not counted in the neural network. We applied the approach to two systems: formic acid C═O stretching and MeCN C≡N stretching vibrational frequency shifts in water. All data sets were prepared using the quantum vibration perturbation approach. Effects of different region divisions, one-body correction, cut range, and training data size were tested. The model with a single-molecule "probe region" showed stable accuracy; it ran roughly 10 times faster than regular deep potential and reduced the training time by about four. The approach is efficient, easy to apply, and extendable to calculating various spectra.

Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation

The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.

Ruthenium hydrides encapsulated in sol–gel glasses exhibit new ultrafast vibrational dynamics

Vibrational dynamics were measured by IR pump–probe spectroscopy and two-dimensional IR spectroscopy for triruthenium dodecacarbonyl and the undecacarbonyl hydride that forms when it is encapsulated in an alumina sol–gel glass. For comparison, a triruthenium undecacarbonyl hydride salt was also synthesized and studied in neat solution to identify the potential influence of the confined solvent environment on the dynamics experienced by carbon monoxide ligands. The vibrational lifetime was found to be significantly decreased for both hydride species relative to the dodecacarbonyl compound. Conversely, spectral diffusion of the CO vibrations was measured to be faster for the parent compound. The most significant dynamic changes occurred upon transformation from the starting compound to the hydride, while only minor differences were observed between the dynamics of the freely dissolved and sol–gel encapsulated hydrides. The results suggest that the structural change to the hydride has the largest impact on the dynamics and that its improved catalytic properties likely do not originate from confined solvent effects.

Origin of thiocyanate spectral shifts in water and organic solvents

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.

Quantum vibration perturbation approach with polyatomic probe in simulating infrared spectra

The quantitative prediction of vibrational spectra of chromophore molecules in solution is challenging and numerous methods have been developed. In this work, we present a quantum vibration perturbation (QVP) approach, which is a procedure that combines molecular quantum vibration and molecular dynamics with perturbation theory. In this framework, an initial Newtonian molecular dynamics simulation is performed, followed by a substitution process to embed molecular quantum vibrational wave functions into the trajectory. The instantaneous vibrational frequency shift at each time step is calculated using the Rayleigh-Schrödinger perturbation theory, where the perturbation operator is the difference in the vibrational potential between the reference chromophore and the perturbed chromophore in the environment. Semi-classical statistical mechanics is employed to obtain the spectral lineshape function. We validated our method using HCOOH·nH₂O (n = 1-2) clusters and HCOOH aqueous solution as examples. The QVP method can be employed for rapid prediction of the vibrational spectrum of a specific mode in solution.

Variational Energy Decomposition Analysis of Charge-Transfer Interactions between Metals and Ligands in Carbonyl Complexes

Variational energy decomposition analyses have been presented to quantify the σ-dative, ligand-to-metal forward charge transfer (CT) and the π-conjugative, metal-to-ligand backward charge delocalization on a series of isolelectronic transition-metal carbonyl complexes M(CO)₆, including M = Ti^2-, V^-, Cr, Mn⁺, and Fe²⁺. Although the qualitative features of these energy terms are understood, well-defined quantitative studies have been scarce. Consistent with early findings, electrostatic and Pauli exchange effects play a key role in σ-donation, resulting in blue shifts in ligand vibrational frequency in the complex geometries. Excluding chemical bonding interactions between the CO ligand and the metal fragments in the energy decomposition analysis, we found that loosely bound electrostatic complexes can be formed at a longer metal-to-ligand distance due to the exponential decay of Pauli exchange. In all complexes, the overall binding stabilization can be attributed to CT effects, with opposing trends between σ-donation and π-back bonding that follows an order of Ti^2- (4.4) > V^1- (2.6) > Cr (1.5) > Mn¹⁺ (1.1) > Fe²⁺ (0.5) in π-to-σ CT ratio. These electronic and energetic features are mirrored in the vibrational frequency shifts induced by different factors. The present investigation may help stimulate the use of energy decomposition techniques to understand the structure and activity of metallocatalysts using density functional theory.

The role of ultrafast structural dynamics with physical and chemical changes in polydimethylsiloxane thin films by two-dimensional IR spectroscopy

Fourier transform infrared (FTIR) and two-dimensional IR (2D-IR) spectroscopies were applied to polydimethylsiloxane (PDMS) cross-linked elastomer films. The vibrational probe for the systems studied was a silicon hydride mode that was covalently bound to the polymer chains. The structure and dynamics reported by this mode were measured in response to a wide range of chemical and physical perturbations, including elevated curing temperature, increased curing agent concentration, mechanical compression, and cooling to near the glass transition temperature. The FTIR spectra were found to be relatively insensitive to all of these perturbations, and 2D-IR spectroscopy revealed that this was due to the overwhelming influence of heterogeneity on the spectral line shape. Surprisingly, the deconvoluted spectral line shapes showed that there were only slight differences in the heterogeneous and homogeneous dynamics even with the drastic macroscopic changes occurring in different systems. In the context of modeling polymer behavior, the results confirm that dynamics on the ultrafast time scale need not be included to properly model PDMS elasticity.