Recovering Intrinsic Fragmental Vibrations Using the Generalized Subsystem Vibrational Analysis

Fast vibrational analysis of molecular systems

The development of infrared difference spectroscopy provides unprecedented insights on structures of complex molecules like metalloproteins. However, the relevant information can be hard to find among the many bands of the vibrational spectra. The ab initio modeling is very helpful to assign the frequencies to vibrational modes but it is a challenge to process the huge quantity of data into descriptors useful for experimentalists. To this end, we developed a new tool called VIBMOL allowing to analyze vibrational modes of molecules from hessian matrices calculated with common quantum chemistry codes. VIBMOL program runs on Unix machines. Through a new graphical interface, the users can calculate the normal modes of molecules, visualize them, simulate infrared spectra, and explore the Potential Energy Distribution of normal modes among any set of vibration coordinates. It is combined with an interface program (gosdmu) formatting relevant data from the GAUSSIAN program. VIBMOL code is available upon request to the authors. A discussion is provided to help the readers to choose between a large choice of different software and it shows how VIBMOL can make the IR assignment easier in the context of collaborations with experimentalists.

Chemical bonding in Uranium-based materials: A local vibrational mode case study of Cs 2 UO 2 Cl 4 and UCl 4 crystals

The Local Vibrational Mode Analysis, initially applied to diverse molecular systems, was extended to periodic systems in 2019. This work introduces an enhanced version of the LModeA software, specifically designed for the comprehensive analysis of two and three-dimensional periodic structures. Notably, a novel interface with the Crystal package was established, enabling a seamless transition from molecules to periodic systems using a unified methodology. Two distinct sets of uranium-based systems were investigated: (i) the evolution of the Uranyl ion (UO  2 2 + ) traced from its molecular configurations to the solid state, exemplified by Cs  2 UO  2 Cl  4 and (ii) Uranium tetrachloride (UCl  4 ) in both its molecular and crystalline forms. The primary focus was on exploring the impact of crystal packing on key properties, including IR and Raman spectra, structural parameters, and an in-depth assessment of bond strength utilizing local mode perspectives. This work not only demonstrates the adaptability and versatility of LModeA for periodic systems but also highlights its potential for gaining insights into complex materials and aiding in the design of new materials through fine-tuning.

Exploring Jahn-Teller distortions: a local vibrational mode perspective

The characterization of normal mode (CNM) procedure coupled with an adiabatic connection scheme (ACS) between local and normal vibrational modes, both being a part of the Local Vibrational Mode theory developed in our group, can identify spectral changes as structural fingerprints that monitor symmetry alterations, such as those caused by Jahn-Teller (JT) distortions. Employing the PBE0/Def2-TZVP level of theory, we investigated in this proof-of-concept study the hexaaquachromium cation case,[ Cr ( OH 2 ) 6 ] 3 + /[ Cr ( OH 2 ) 6 ] 2 + , as a commonly known example for a JT distortion, followed by the more difficult ferrous and ferric hexacyanide anion case,[ Fe ( CN ) 6 ] 4 - /[ Fe ( CN ) 6 ] 3 - . We found that in both cases CNM of the characteristic normal vibrational modes reflects delocalization consistent with high symmetry and ACS confirms symmetry breaking, as evidenced by the separation of axial and equatorial group frequencies. As underlined by the Cremer-Kraka criterion for covalent bonding, from[ Cr ( OH 2 ) 6 ] 3 + to[ Cr ( OH 2 ) 6 ] 2 + there is an increase in axial covalency whereas the equatorial bonds shift toward electrostatic character. From[ Fe ( CN ) 6 ] 4 - to[ Fe ( CN ) 6 ] 3 - we observed an increase in covalency without altering the bond nature. Distinct π back-donation disparity could be confirmed by comparison with the isolated CN- system. In summary, our study positions the CNM/ACS protocol as a robust tool for investigating less-explored JT distortions, paving the way for future applications.

Ferroptosis-Related lncRNAs Act as Novel Prognostic Biomarkers in the Gastric Adenocarcinoma Microenvironment, Immunotherapy, and Chemotherapy

Ferroptosis, a form of programmed cell death akin to necrosis, is managed by iron and is distinguished by lipid peroxidation. Gastric cancer is a highly aggressive form of cancer, responsible for the third highest number of cancer-related deaths globally. Despite this, the potential of ferroptosis to predict the occurrence of this cancer is yet to be determined. In this research, a comprehensive examination was conducted to explore the link between long noncoding RNAs (lncRNAs) and ferroptosis, in order to uncover an lncRNA signature that can predict drug susceptibility and tumor mutational burden (TMB) in gastric adenocarcinoma. We conducted an in-depth analysis of the GC immune microenvironment and immunotherapy, with a particular focus on ferroptosis-related lncRNA prognostic biomarkers, and further explored the correlation between these factors and prognosis, immune infiltration, single nucleotide variation (SNV), and drug sensitivity for gastric adenocarcinoma patients. Through our investigations, we have discovered five lncRNA signatures related to ferroptosis that can accurately forecast the prognosis of gastric adenocarcinoma patients and also regulate the proliferation, migration, and occurrence of ferroptosis in gastric adenocarcinoma cells. In conclusion, this lncRNA signature associated with ferroptosis may be employed as a prognostic indicator for gastric adenocarcinoma, thus presenting a potential solution.

Quantitative proteomic profiling of hepatocellular carcinoma at different serum alpha-fetoprotein level

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Serum AFP equal to 400 ng/mL is a pivotal turning point not only in prognosis but also metabolic and invasion associated pathways.

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Adjacent noncancerous tissues are not biological normal components at protein level.

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Four druggable targets (C1QBP, HSPE1, CHDH, ITGAL) are identified as potential prognostic biomarkers in hepatocellular carcinoma.

Purpose

Hepatocellular carcinoma (HCC) is characterized by a poor long-term prognosis and high mortality rate. Serum alpha-fetoprotein (AFP) levels show great prognostic value in patients undergoing hepatectomy. This study aims to explore proteomic profiling in HCC samples based on AFP subgroups and identify potential key targets involved in HCC progression.

Methods

Twelve paired tumor and adjacent noncancerous tissue samples were collected from patients with HCC who underwent primary curative resection from January 2012 to December 2013. Clinical information was curated from four tissue microarrays to conduct survival analysis based on serum AFP levels. TMT-based quantitative proteomic analyses and bioinformatics analyses were performed to comprehensively profile molecular features. Immunohistochemistry was carried out to validate protein expression of identified targets. Kaplan-Meier survival analysis was performed to assess the overall survival and recurrence-free survival based on protein expressions.

Results

AFP (400 ng/mL) was a turning point in prognosis, metabolic- and invasion-associated pathways. The mass spectrometry analysis yielded a total of 5573 identified proteins. Annotations of 151 differentially expressed proteins in tumors and 95 proteins in paracancerous tissues (1.2-fold) showed similarities in biological processes, cellular components, molecular functions. Furthermore, differentially expressed hub proteins with five innovatively nominated druggable targets (C1QBP, HSPE1, GLUD2 for tumors and CHDH, ITGAL for paracancerous tissues), of which four (C1QBP, HSPE1, CHDH, ITGAL) targets were associated with poor overall survival (all Log-rank P < 0.05).

Conclusions

Our quantitative proteomics analyses identified four key prognostic biomarkers in HCC and provide opportunities for translational medicine and new treatment.

Assessing the Intrinsic Strengths of Ion–Solvent and Solvent–Solvent Interactions for Hydrated Mg2+ Clusters

Information resulting from a comprehensive investigation into the intrinsic strengths of hydrated divalent magnesium clusters is useful for elucidating the role of aqueous solvents on the Mg2+ ion, which can be related to those in bulk aqueous solution. However, the intrinsic Mg–O and intermolecular hydrogen bond interactions of hydrated magnesium ion clusters have yet to be quantitatively measured. In this work, we investigated a set of 17 hydrated divalent magnesium clusters by means of local vibrational mode force constants calculated at the ωB97X-D/6-311++G(d,p) level of theory, where the nature of the ion–solvent and solvent–solvent interactions were interpreted from topological electron density analysis and natural population analysis. We found the intrinsic strength of inner shell Mg–O interactions for [Mg(H2O)n]2+ (n = 1–6) clusters to relate to the electron density at the bond critical point in Mg–O bonds. From the application of a secondary hydration shell to [Mg(H2O)n]2+ (n = 5–6) clusters, stronger Mg–O interactions were observed to correspond to larger instances of charge transfer between the lp(O) orbitals of the inner hydration shell and the unfilled valence shell of Mg. As the charge transfer between water molecules of the first and second solvent shell increased, so did the strength of their intermolecular hydrogen bonds (HBs). Cumulative local vibrational mode force constants of explicitly solvated Mg2+, having an outer hydration shell, reveal a CN of 5, rather than a CN of 6, to yield slightly more stable configurations in some instances. However, the cumulative local mode stretching force constants of implicitly solvated Mg2+ show the six-coordinated cluster to be the most stable. These results show that such intrinsic bond strength measures for Mg–O and HBs offer an effective way for determining the coordination number of hydrated magnesium ion clusters.

A revised formulation of the generalized subsystem vibrational analysis (GSVA)

In this work, a simplified formulation of our recently developed generalized subsystem vibrational analysis (GSVA) for obtaining intrinsic fragmental vibrations (J Chem Theory Comput 14:2558, 2018) is presented. In contrast to the earlier implementation, which requires the explicit definition of a non-redundant set of internal coordinate parameters to be constructed for the subsystem, the new implementation circumvents this process by employing massless Eckart conditions to the subsystem fragment paired with a Gram-Schmidt orthogonalization to span the same internal vibration space indirectly. This revised version of GSVA (rev-GSVA) can be applied to equilibrium structure as well as transition state structure, and it has been incorporated into the open-source package UniMoVib (https://github.com/zorkzou/UniMoVib).

Supplementary Information

The online version contains supplementary material available at 10.1007/s00214-021-02727-y.

Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome

Infrared (IR) spectroscopy is an undoubtedly valuable tool for analyzing vibrations, conformational changes, and chemical reactions of biological macromolecules. Currently, there is a lack of theoretical methods to create a model successfully and efficiently simulate and interpret the origin of the spectral signatures, which are often complex to analyze. Here, we develop a new method for IR vibrational spectroscopy based on analytic second derivatives of electrostatic embedding QM/MM energy, the computation of electric dipole moments with respect to nuclear perturbations and the localization of normal modes. In addition to the IR spectrum, the method can provide the origin of each peak from clearly identified molecular motions of constituent fragments. As a proof of concept, we analyze the IR spectra of flavin adenine dinucleotides in water and in Arabidopsis thaliana cryptochrome proteins for four redox forms, in addition to the difference IR spectra before and after illumination with blue light. We show that the main peaks in the difference spectrum are due to N-H hydrogen out-of-plane motions and hydrogen bendings.

Local vibrational mode analysis of ion-solvent and solvent-solvent interactions for hydrated Ca2+ clusters

Hydrated calcium ion clusters have received considerable attention due to their essential role in biological processes such as bone development, hormone regulation, blood coagulation, and neuronal signaling. To better understand the biological role of the cation, the interactions between the Ca²⁺ ions and water molecules have been frequently investigated. However, a quantitative measure for the intrinsic Ca-O (ion-solvent) and intermolecular hydrogen bond (solvent-solvent) interactions has been missing so far. Here, we report a topological electron density analysis and a natural population analysis to analyze the nature of these interactions for a set of 14 hydrated calcium clusters via local mode stretching force constants obtained at the ωB97X-D/6-311++G(d,p) level of theory. The results revealed that the strength of inner Ca-O interactions for Ca(H₂O)_n ²⁺ (n = 1-8) clusters correlates with the electron density. The application of a second hydration shell to Ca(H₂O)_n ²⁺ (n = 6-8) clusters resulted in stronger Ca-O interactions where a larger electron charge transfer between lp(O) of the first hydration shell and the lower valence of Ca prevailed. The strength of the intermolecular hydrogen bonds, formed between the first and second hydration shells, became stronger when the charge transfers between hydrogen bond (HB) donors and HB acceptors were enhanced. From the local mode stretching force constants of implicitly and explicitly solvated Ca²⁺, we found the six-coordinated cluster to possess the strongest stabilizations, and these results prove that the intrinsic bond strength measures for Ca-O and hydrogen bond interactions form new effective tools to predict the coordination number for the hydrated calcium ion clusters.

PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids

Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q-Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.

Anharmonic quantum nuclear densities from full dimensional vibrational eigenfunctions with application to protonated glycine

The interpretation of molecular vibrational spectroscopic signals in terms of atomic motion is essential to understand molecular mechanisms and for chemical characterization. The signals are usually assigned after harmonic normal mode analysis, even if molecular vibrations are known to be anharmonic. Here we obtain the quantum anharmonic vibrational eigenfunctions of the 11-atom protonated glycine molecule and we calculate the density distribution of its nuclei and its geometry parameters, for both the ground and the O-H stretch excited states, using our semiclassical method based on ab initio molecular dynamics trajectories. Our quantum mechanical results describe a molecule elongated and more flexible with respect to what previously thought. More importantly, our method is able to assign each spectral peak in vibrational spectroscopy by showing quantitatively how normal modes involving different functional groups cooperate to originate that spectroscopic signal. The method will possibly allow for a better rationalization of experimental spectroscopy.

A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory

Over the past two decades, the vibrational Stark effect has become an important tool to measure and analyze the in situ electric field strength in various chemical environments with infrared spectroscopy. The underlying assumption of this effect is that the normal stretching mode of a target bond such as CO or CN of a reporter molecule (termed vibrational Stark effect probe) is localized and free from mass-coupling from other internal coordinates, so that its frequency shift directly reflects the influence of the vicinal electric field. However, the validity of this essential assumption has never been assessed. Given the fact that normal modes are generally delocalized because of mass-coupling, this analysis was overdue. Therefore, we carried out a comprehensive evaluation of 68 vibrational Stark effect probes and candidates to quantify the degree to which their target normal vibration of probe bond stretching is decoupled from local vibrations driven by other internal coordinates. The unique tool we used is the local mode analysis originally introduced by Konkoli and Cremer, in particular the decomposition of normal modes into local mode contributions. Based on our results, we recommend 31 polyatomic molecules with localized target bonds as ideal vibrational Stark effect probe candidates.

Describing Polytopal Rearrangements of Fluxional Molecules with Curvilinear Coordinates Derived from Normal Vibrational Modes: A Conceptual Extension of Cremer-Pople Puckering Coordinates

In this work a new curvilinear coordinate system is presented for the comprehensive description of polytopal rearrangements of N-coordinate compounds (N = 4-7) and systems containing an N-coordinate subunit. It is based on normal vibrational modes and a natural extension of the Cremer-Pople puckering coordinates ( J. Am. Chem. Soc. 1975, 97, 1354) together with the Zou-Izotov-Cremer deformation coordinates ( J. Phys. Chem. A 2011, 115, 8731) for ring structures to N-coordinate systems. We demonstrate that the new curvilinear coordinates are ideal reaction coordinates describing fluxional rearrangement pathways by revisiting the Berry pseudorotation and the lever mechanism in sulfur tetrafluoride, the Berry pseudorotation and two Muetterties' mechanisms in pentavalent compounds, the chimeric pseudorotation in iodine pentafluoride, Bailar and Ray-Dutt twists in hexacoordinate tris-chelates as well as the Bartell mechanism in iodine heptafluoride. The results of our study reveal that this dedicated curvilinear coordinate system can be applied to most coordination compounds opening new ways for the systematic modeling of fluxional processes.

In Situ Assessment of Intrinsic Strength of X-I⋯OA-Type Halogen Bonds in Molecular Crystals with Periodic Local Vibrational Mode Theory

Periodic local vibrational modes were calculated with the rev-vdW-DF2 density functional to quantify the intrinsic strength of the X-I⋯OA-type halogen bonding (X = I or Cl; OA: carbonyl, ether and N-oxide groups) in 32 model systems originating from 20 molecular crystals. We found that the halogen bonding between the donor dihalogen X-I and the wide collection of acceptor molecules OA features considerable variations of the local stretching force constants (0.1–0.8 mdyn/Å) for I⋯O halogen bonds, demonstrating its powerful tunability in bond strength. Strong correlations between bond length and local stretching force constant were observed in crystals for both the donor X-I bonds and I⋯O halogen bonds, extending for the first time the generalized Badger’s rule to crystals. It is demonstrated that the halogen atom X controlling the electrostatic attraction between the σ-hole on atom I and the acceptor atom O dominates the intrinsic strength of I⋯O halogen bonds. Different oxygen-containing acceptor molecules OA and even subtle changes induced by substituents can tweak the n→σ∗(X-I) charge transfer character, which is the second important factor determining the I⋯O bond strength. In addition, the presence of the second halogen bond with atom X of the donor X-I bond in crystals can substantially weaken the target I⋯O halogen bond. In summary, this study performing the in situ measurement of halogen bonding strength in crystalline structures demonstrates the vast potential of the periodic local vibrational mode theory for characterizing and understanding non-covalent interactions in materials.

A Continuum from Halogen Bonds to Covalent Bonds: Where Do λ3 Iodanes Fit?

The intrinsic bonding nature of λ 3 -iodanes was investigated to determine where its hypervalent bonds fit along the spectrum between halogen bonding and covalent bonding. Density functional theory with an augmented Dunning valence triple zeta basis set ( ω B97X-D/aug-cc-pVTZ) coupled with vibrational spectroscopy was utilized to study a diverse set of 34 hypervalent iodine compounds. This level of theory was rationalized by comparing computational and experimental data for a small set of closely-related and well-studied iodine molecules and by a comparison with CCSD(T)/aug-cc-pVTZ results for a subset of the investigated iodine compounds. Axial bonds in λ 3 -iodanes fit between the three-center four-electron bond, as observed for the trihalide species IF 2 − and the covalent FI molecule. The equatorial bonds in λ 3 -iodanes are of a covalent nature. We explored how the equatorial ligand and axial substituents affect the chemical properties of λ 3 -iodanes by analyzing natural bond orbital charges, local vibrational modes, the covalent/electrostatic character, and the three-center four-electron bonding character. In summary, our results show for the first time that there is a smooth transition between halogen bonding → 3c–4e bonding in trihalides → 3c–4e bonding in hypervalent iodine compounds → covalent bonding, opening a manifold of new avenues for the design of hypervalent iodine compounds with specific properties.

Improving Vibrational Mode Interpretation Using Bayesian Regression

To streamline the interpretation of vibrational spectra, this work introduces the use of Bayesian linear regression with automatic relevance determination as a viable approach to decompose the atomic motions along any vibrational mode as a weighted combination of displacements along chemically meaningful internal coordinates. This novel approach denominated vibrational mode automatic relevance determination (VMARD) is presented and compared with the well-established potential energy decomposition (PED) scheme. Good agreement is generally attained between the two methods. VMARD returns a decomposition of the atomic displacement using only a small number of internal coordinates, thus aiding the interpretation of the vibrational spectra. Moreover, the results show that the VMARD descriptions are resilient toward the addition of additional internal coordinates, achieving a concise description of the vibrational modes despite the use of redundant internal coordinates. Potential applications of VMARD involving the gathering of physical insights on the atomic motions along the reaction coordinate at transition state structures, as well as the improvement of theoretically predicted vibrational frequencies, are also presented under a proof-of-concept perspective.

The Astrochemistry Implications of Quantum Chemical Normal Modes Vibrational Analysis

Understanding the molecular vibrations underlying each of the unknown infrared emission (UIE) bands (such as those found at 3.3, 3.4, 3.5, 6.2, 6.9, 7.7, 11.3, 15.8, 16.4, 18.9 μ m) observed in or towards astronomical objects is a vital link to uncover the molecular identity of their carriers. This is usually done by customary classifications of normal-mode frequencies such as stretching, deformation, rocking, wagging, skeletal mode, etc. A large literature on this subject exists and since 1952 ambiguities in classifications of normal modes via this empirical approach were pointed out by Morino and Kuchitsu New ways of interpretation and analyzing vibrational spectra were sought within the theoretical framework of quantum chemistry. Many of these methods cannot easily be applied to the large, complex molecular systems which are one of the key research interests of astrochemistry. In considering this demand, a simple and new method of analyzing and classifying the normal mode vibrational motions of molecular systems was introduced. This approach is a fully quantitative method of analysis of normal-mode displacement vector matrices and classification of the characteristic frequencies (fundamentals) underlying the observed IR bands. Outcomes of applying such an approach show some overlap with customary empirical classifications, usually at short wavelengths. It provides a quantitative breakdown of a complex vibration (at longer wavelengths) into the contributed fragments such as their aromatic or aliphatic components. In addition, in molecular systems outside the classical models of chemical bonds and structures where the empirical approach cannot be applied, this quantitative method enables an interpretation of vibrational motion(s) underlying the IR bands. As a result, further modifications in the structures (modeling) and the generation of the IR spectra (simulating) of the UIE carriers, initiated by proposing a PAH model, can be implemented in an efficient way. Here fresh results on the vibrational origin of the spectacular UIE bands based on astrochemistry molecular models, explored through the lens of the quantitative method applied to thousands of different vibrational motion matrices are discussed. These results are important in the context of protoplanetary nebulae and planetary nebulae where various molecular species have been uncovered despite their harsh environments.