Searching low-energy conformers of neutral and protonated di-, tri-, and tetra-glycine using first-principles accuracy assisted by the use of neural network potentials.

In the last ten years, combinations of state-of-the-art gas-phase spectroscopies and quantum chemistry calculations have suggested several intuitive trends in the structure of small polypeptides that may not hold true. For example, the preference for the cis form of the peptide bond and multiple protonated sites was proposed by comparing experimental spectra with low-energy minima obtained from limited structural sampling using various density functional theory methods. For understanding the structures of polypeptides, extensive sampling of their configurational space with high-accuracy computational methods is required. In this work, we demonstrated the use of deep-learning neural network potential (DL-NNP) to assist in exploring the structure and energy landscape of di-, tri-, and tetra-glycine with the accuracy of high-level quantum chemistry methods, and low-energy conformers of small polypeptides can be efficiently located. We hope that the structures of these polypeptides we found and our preliminary analysis will stimulate further experimental investigations.

A first-principles exploration of the conformational space of sodiated di-saccharides assisted by semi-empirical methods and neural network potentials.

Previous exploration of the conformational space of sodiated mono-saccharides using a random search algorithm leads to ∼103 structurally distinct conformers covering an energy range of ∼150 kJ mol-1. Thus, it is reasonable to expect that the number of distinct conformers for a given disaccharide would be on the order of 106. Efficient identification of distinct conformers at the first-principles level has been demonstrated with the assistance of neural network potential (NNP) with an accuracy of ∼1 kJ mol-1 compared to DFT. Leveraging a local minima database of neutral and sodiated glucose (Glc), we develop algorithms to systematically explore the conformation landscape of 19 Glc-based sodiated disaccharides. To accelerate the exploration, the NNP method is implemented. The NNP achieves an accuracy of ∼2.3 kJ mol-1 compared to DFT, offering a comparable quality to that of DFT. Through a multi-model approach integrating DFTB3, NNP and DFT, we can rapidly locate low-energy disaccharide conformers at the first-principles level. The methodology we show here can be used to efficiently explore the potential energy landscape of any di-saccharides when first-principles accuracy is required.

Near-infrared spectroscopy of H3O+⋯Xn (X = Ar, N2, and CO, n = 1-3).

Near-infrared (NIR) spectra of H3O+⋯Xn (X = Ar, N2, and CO, n = 1-3) in the first overtone region of OH-stretching vibrations (4800-7000 cm-1) were measured. Not only OH-stretching overtones but also several combination bands are major features in this region, and assignments of these observed bands are not obvious at a glance. High-precision anharmonic vibrational simulations based on the discrete variable representation approach were performed. The simulated spectra show good agreement with the observed ones and provide firm assignments of the observed bands, except in the case of X = CO, in which higher order vibrational mode couplings seem significant. This agreement demonstrates that the present system can be a benchmark for high precision anharmonic vibrational computations of NIR spectra. Band broadening in the observed spectra becomes remarkable with an increase of the interaction with the solvent molecule (X). The origin of the band broadening is explored by rare gas tagging experiments and anharmonic vibrational simulations of hot bands.

Modulation of the strength of weak S-H⋯O hydrogen-bond: Spectroscopic study of the complexes of 2-flurothiophenol with methanol and ethanol.

Spectroscopic exploration of sulfur-centered hydrogen bonding involving a thiol group (S-H) as the hydrogen bond donor is scarce in the literature. Herein, we have investigated 1:1 complexes of 2-fluorothiophenol (2-FTP) with methanol (MeOH) and ethanol (EtOH) in the gas phase to examine the physical characteristics and strength of the S-H⋯O hydrogen bond. Structures, conformations, and the strength of the S-H⋯O interaction are investigated by measuring the electronic and Infrared (IR) spectra of the two complexes employing resonant two-photon ionization, UV-UV hole-burning, and IR-UV double resonance spectroscopic techniques combined with quantum chemical calculations. Three conformers of 2-FTP⋯MeOH and two conformers of 2-FTP⋯EtOH have been detected in the experiment. A comparison of the IR spectra obtained from the experiment with those of the low-energy conformers of 2-FTP⋯MeOH and 2-FTP⋯EtOH predicted from the theory confirms that all the observed conformers of the two complexes are primarily S-H⋯O hydrogen bonded. The IR red-shifts found in the S-H stretching frequencies in 2-FTP⋯MeOH and 2-FTP⋯EtOH concerning that in 2-FTP are ∼76 and ∼88 cm-1, respectively, which are much larger than that was reported earlier in the 2-FTP⋯H2O complex (30 cm-1). The strength and physical nature of different noncovalent interactions, including the S-H⋯O hydrogen bond existing in the complexes, are further analyzed using natural bond orbital analysis, quantum theory of atoms in molecules, and localized molecular orbital-energy decomposition analysis. The current investigation reveals that the S-H⋯O hydrogen bond can be strengthened by judicial choices of the hydrogen bond acceptors of higher proton affinities.

A self-adapting first-principles exploration on the dissociation mechanism in sodiated aldohexose pyranoses assisted with neural network potentials.

Understanding the mechanism of collision-induced dissociation (CID) in mono-saccharides with density functional theory (DFT) is challenging because of many possible reaction paths that originate from their high structural diversity. To search for the transition state (TS) from the huge number of conformers, we propose a three-step search scheme with the assistance of neural network potential (NNP). The search starts from a cross-checking of sugars, to a global search of all possible channels, and in the end, an exhaustive exploration around the low-lying channels. The cross-checking step quickly adapts the NNP from the studied molecules to the target ones. The other two steps utilize the adapted NNP to find the available pathways via random sampling of the structures. The study of the CID reactions in all eight types of aldohexose pyranoses was applied using the search scheme. The DFT calculations on AH-0 (Glc, Gal, and Man) in the previous study were utilized to construct an NNP and provide the TS structure database for searching AH-1 (All, Alt, Gul, Ido, and Tal). In total, we identified around 5200 TSs in AH-0 and AH-1, and the final NNP covers an energy range of more than 500 kJ mol-1 with a mean absolute error of energy less than 4 kJ mol-1. The search scheme is useful not only for saccharides but also for highly flexible bio-molecules.

A first-principles exploration of the conformational space of sodiated pyranose assisted by neural network potentials.

Sampling the conformational space of monosaccharides using the first-principles methods is important and as a database of local minima provides a solid base for interpreting experimental measurements such as infrared photo-dissociation (IRPD) spectroscopy or collision-induced dissociation (CID). IRPD emphasizes low-energy conformers and CID can distinguish conformers with distinct reaction pathways. A typical computational approach is to engage empirical or semi-empirical methods to sample the conformational space first, and only selected minima are reoptimized at first-principles levels. In this work, we propose a computational scheme to explore the configurational space of 12 types of sodiated pyranoses with the assistance of a neural network potential (NNP). We demonstrated that it is possible to train an NNP based on the density functional calculations extracted from a previous study on sodiated glucose (Glc), galactose (Gal), and mannose (Man). This NNP yields a better description of the other five types of aldohexoses than the four types of ketohexoses. We further show that such a discrepancy in the accuracy of NNP can be resolved by an active learning scheme where the NNP model is engaged in generating the data and has itself updated. Through this iterative process, we can locate more than 17 000 distinct local minima at the B3LYP/6-311+G(d,p) level and an NNP with an accuracy of 1 kJ mol-1 was created, which can be used for further studies.

Approaching the "Zundel" Limit: Tuning the Vibrational Coupling in N2H+Ng, Ng = {He, Ne, Ar, Kr, Xe, and Rn}.

The diazenylium ion (N2H+) is a ubiquitous ion in dense molecular clouds. This ion is often used as a dense gas tracer in outer space. Most of the previous works on diazenylium ion have focused on the shared-proton stretch band, νH+. In this work, we have performed reduced-dimensional calculations to investigate the vibrational structure of N2H+Ng, Ng = {He, Ne, Ar, Kr, Xe, and Rn}. We demonstrate a few interesting things about this system. First, the vibrational coupling in N2H+ can be tuned to switch on interesting anharmonic effects such as Fermi resonance or combination bands by tagging it with different noble gases. Second, a comparison of the vibrational spectrum from N2H+He to N2H+Rn shows that the νH+ can be swept from an "Eigen-like" to a "Zundel-like" limiting case. Anharmonic calculations were performed using a multilevel approach, which utilized the MP2 and CCSD(T) levels of theories. Binding energies for the elimination of Ng in N2H+Ng are also reported.

Structures of (Pyrazine)2 and (Pyrazine)(Benzene) Dimers Investigated with Infrared-Vacuum Ultraviolet Spectroscopy and Quantum-Chemical Calculations: Competition among π-π, CH···π, and CH···N Interactions.

The structures of a pyrazine dimer (pyrazine)2 and (pyrazine)(benzene) hetero-dimer cooled in a supersonic beam were investigated by the measurement of the infrared spectra in the C-H stretching region with infrared-vacuum ultraviolet (IR-VUV) spectroscopy and quantum-chemical calculations. The stabilization energy calculation at the CCSD(T)/aug-cc-pVTZ level of theory predicted three isomers for (pyrazine)2 and three for (pyrazine)(benzene) with energy within 6 kJ/mol. Among them, the cross-displaced π-π stacked structure is the most stable in both dimers. In the observed IR spectra, both dimers exhibited two intense bands near 3065 cm-1, with intervals of 8 cm-1 in (pyrazine)2 and 11 cm-1 in (pyrazine)(benzene), while only one band appeared in the monomer. For (pyrazine)(benzene), we also measured the IR spectrum of (pyrazine)(benzene-d6), where the interval of the two bands was unchanged. The analysis of the observed IR spectra with anharmonic calculations suggested the coexistence of three isomers of (pyrazine)2 and (pyrazine)(benzene) in a supersonic jet. For (pyrazine)2, the two isomers which were previously assigned to the H-bonded planar and the π-π stacked structures respectively were reassigned to the cross-displaced π-π stacked and T-shaped structures, respectively. In addition, the quantum chemical calculation and IR-VUV spectral measurement suggested the coexistence of the H-bonded planar isomer in the jet. For (pyrazine)(benzene), the IR spectrum of the (pyrazine) site showed a similar spectral pattern to that of (pyrazine)2, especially the split at ∼3065 cm-1. However, the anharmonic analysis suggested that they are assigned to the different vibrational motions of (pyrazine). The anharmonic vibrational analysis is essential to associate the observed IR spectra with the correct structures of the dimer.

Ab initio anharmonic analysis of complex vibrational spectra of phenylacetylene and fluorophenylacetylenes in the acetylenic and aromatic C-H stretching region.

Vibrational spectra in the acetylenic and aromatic C-H stretching regions of phenylacetylene and fluorophenylacetylenes, viz., 2-fluorophenylacetylene, 3-fluorophenylacetylene, and 4-fluorophenylacetylene, were measured using the IR-UV double resonance spectroscopic method. The spectra, in both acetylenic and aromatic C-H stretching regions, were complex exhibiting multiple bands. Ab-initio anharmonic calculations with quartic potential using B97D3/6-311++G(d,p) and vibrational configuration interaction were able to capture all important spectral features in both the regions of the experimentally observed spectra for all four molecules considered in the present work. Interestingly, for phenylacetylene, the spectrum in the acetylenic C-H stretching region emerges due to anharmonic coupling of modes localized on the acetylenic moiety along with the other ring modes, which also involve displacements on the acetylenic group, which is in contrast to what has been proposed and propagated in the literature. In general, this coupling scheme is invariant to the fluorine atom substitution. For the aromatic C-H stretching region, the observed spectrum emerges due to the coupling of the C-H stretching with C-C stretching and C-H in-plane bending modes.

Anharmonic IR spectra of solvated ammonium and aminium ions: resemblance between water and bisulfate solvations.

In this work, we analyze the vibrational spectra of ammonium, methylammonium, and dimethylammonium ions solvated by either water molecules or bisulfate anions using anharmonic vibrational algorithms. Rich and complicated spectral features in the 2700-3200 cm-1 region of the experimental spectra of these clusters are attributed to originate from strong Fermi resonance between hydrogen-bonded NH stretching fundamentals and NH bending overtones. Additional weaker bands around 2500-2600 cm-1 in solvated aminium ions are assigned to the combination tones involving the CH-NH (methyl-amino) rocking modes. Furthermore, the qualitative resemblance in band positions and spectral patterns between two-water-solvated and two-bisulfate-solvated cations suggest a common vibrational coupling scheme beneath the two seemingly different micro-solvation environments.

Infrared spectroscopy and theoretical structure analyses of protonated fluoroalcohol clusters: the impact of fluorination on the hydrogen bond networks.

To explore the impact of fluorination on the hydrogen bond networks of protonated alkylalcohols, infrared spectroscopy and theoretical computations of protonated 2,2,2-trifluoroethanol clusters, H+(TFE)n, (n = 4-7), were performed. It has been demonstrated that the development of the hydrogen bond networks from a linear type to cyclic types occurs in this size region for the protonated alkylalcohol clusters. In contrast, infrared spectroscopy of H+(TFE)n in the OH/CH stretch region clearly indicated that the linear type structures are held in the whole size range, irrespective of temperature of the clusters. The extensive stable isomer structure search of H+(TFE)n based on our latest sampling approach supported the strong preference of the linear type hydrogen bond networks. Detailed analyses of the free OH stretching vibrational bands evidenced the intra- and intermolecular OH⋯FC interactions in the clusters. In addition, infrared spectra of protonated clusters of 2,2-difluoroethanol, 2,2-difluoropropanol, and 3,3,3-trifluoropropanol were measured for n = 4 and 5, and their spectra also indicated the effective inhibition of the cyclic hydrogen bond network formation by the fluorination.

Capturing the potential energy landscape of large size molecular clusters from atomic interactions up to a 4-body system using deep learning.

Exploring the structure and properties of molecular clusters with accuracy using the ab initio methods is a resource intensive task due to the increasing cost of the ab initio methods and the number of distinct conformers as the size increases. The energy landscape of methanol clusters has been previously explored using computationally efficient empirical models to collect a database of structurally distinct minima, followed by re-optimization using ab initio methods. In this work, we propose a new method that utilizes the database of stable conformers and borrow the fragmentation concept of many-body-expansion (MBE) methods in ab initio methods to train a deep-learning machine learning (ML) model using SchNet. Picking 684 local minima of (CH3OH)5 to (CH3OH)8 from the existing database, we can generate ∼51 000 data points of one-body, two-body, three-body and four-body molecular systems to train an ML model to reach a mean absolute error (MAE) of 3.19 kJ mol-1 (in energy) and 2.48 kJ mol-1 Å-1 (in forces) tested against ab initio calculations up to (CH3OH)14. This ML model is then used to create a database of low energy isomers of (CH3OH)n (n = 15-20). The proposed scheme can be applied to other hydrogen bonded molecular clusters with an accuracy of first-principles methods and computational speed of empirical force-fields.

Collision-induced dissociation of Na+-tagged ketohexoses: experimental and computational studies on fructose.

Collision-induced dissociation tandem mass spectrometry (CID-MSn) and computational investigation at the MP2/6-311+G(d,p) level of theory have been employed to study Na+-tagged fructose, an example of a ketohexose featuring four cyclic isomers: α-fructofuranose (αFruf), ß-fructofuranose (ßFruf), α-fructopyranose (αFrup), and ß-fructopyranose (ßFrup). The four isomers can be separated by high-performance liquid chromatography (HPLC) and they show different mass spectra, indicating that CID-MSn can distinguish the different fructose forms. Based on a simulation using a micro-kinetic model, we have obtained an overview of the mechanisms for the different dissociation pathways. It has been demonstrated that the preference for the C-C cleavage over the competing isomerization of linear fructose is the main reason for the previously reported differences between the CID-MS spectra of aldohexoses and ketohexoses. In addition, the kinetic modeling helped to confirm the assignment of the different measured mass spectra to the different fructose isomers. The previously reported assignment based on the peak intensities in the HPLC chromatogram had left some open questions as the preference for the dehydration channels did not always follow trends previously observed for aldohexoses. Setting up the kinetic model further enabled us to directly compare the computational and experimental results, which indicated that the model can reproduce most trends in the differences between the dissociation pathways of the four cyclic fructose isomers.

Spectral Signatures of Protonated Noble Gas Clusters of Ne, Ar, Kr, and Xe: From Monomers to Trimers.

The structures and spectral features of protonated noble gas clusters are examined using a first principles approach. Protonated noble gas monomers (NgH+) and dimers (NgH+Ng) have a linear structure, while the protonated noble gas trimers (Ng3H+) can have a T-shaped or linear structure. Successive binding energies for these complexes are calculated at the CCSD(T)/CBS level of theory. Anharmonic simulations for the dimers and trimers unveil interesting spectral features. The symmetric NgH+Ng are charactized by a set of progression bands, which involves one quantum of the asymmetric Ng-H+ stretch with multiple quanta of the symmetric Ng-H+ stretch. Such a spectral signature is very robust and is predicted to be observed in both T-shaped and linear isomers of Ng3H+. Meanwhile, for selected asymmetric NgH+Ng', a Fermi resonance interaction involving the first overtone of the proton bend with the proton stretch is predicted to occur in ArH+Kr and XeH+Kr.

Lithium and sodium intercalation in a 2D NbSe2 bilayer-stacked homostructure: comparative study of ionic adsorption and diffusion behavior.

In this work, we probed the lithium and sodium intercalation properties in monolayer-stacked NbSe2 bilayer homostructure configurations for their potential application as anode materials in lithium and sodium ion batteries. Similar to known monolayer transition metal dichalcogenides, such as VS2, the structural phase transition barrier of NbSe2 from 1H to 1T is strengthened by lithium and sodium adsorption, implying that it is robust under multiple charging and discharging processes. As multi-layer, stacked 2D materials are more relevant to experiments and their intended applications, four bilayer homostructure stackings were constructed based on the alignment of Nb and Se. All four bilayer homostructure stackings were found to significantly enhance the binding of lithium and sodium at the van der Waals interface, and thus potentially increase the theoretical specific energy capacity of NbSe2via bilayer stacking. In terms of ionic diffusion, it is observed that for all of the bilayer homostructure configurations the diffusion energy barrier for lithium and sodium generally increased compared to the monolayer case. The nature of the stacking appears to affect the diffusion energy barrier with a value of as high as 1.94 eV in the case of sodium for the AB full stacking (compared to 0.08 eV for the monolayer). It is inferred that although the bilayer homostructure stacking of NbSe2 could significantly increase the theoretical specific energy capacity for both lithium and sodium, its drawback is the slowing down of the ion kinetics at the van der Waals interface, which are also important in the charging and discharging processes of a battery system.

Size of the hydrogen bond network in liquid methanol: a quantum cluster equilibrium model with extensive structure search.

Studies have debated what is a favorable cluster size in liquid methanol. Applications of the quantum cluster equilibrium (QCE) model on a limited set of cluster structures have demonstrated the dominance of cyclic hexamers in liquid methanol. In this study, we examined the aforementioned question by integrating our implementation of QCE with a molecular-dynamics-based structural searching scheme. QCE simulations were performed using a database comprising extensively searched stable conformers of (MeOH)n for n = 2-14, which were optimized by B3LYP/6-31+G(d,p) with and without the dispersion correction. Our analysis indicated that an octamer structure can contribute significantly to cluster probability. By reoptimizing selected conformers with high probability at the MP2 level, we found that the aforementioned octamer became the dominant species due to favorable vibrational free energy, which was attributed to modes of intermolecular vibration.

An ab initio anharmonic approach to IR, Raman and SFG spectra of the solvated methylammonium ion.

The methylammonium ion (CH3NH3+, or noted as MA-H+) is one of the smallest organic ammonium ions that play important roles in organic-inorganic halide perovskites. Despite the simple structure, the vibrational spectra of MA-H+ exhibit complicated features in the 3 µm region which are sensitive to the solvation environment. In the present work, we have applied the ab initio anharmonic algorithm at the CCSD/aug-cc-pVDZ level to simulate the IR and Raman spectra of the solvated methylammonium ion, MA-H+⋯X3, where X denotes the solvent molecules, to understand the Fermi resonance mechanism in which the overtones of NH bending modes are coupled with the fundamentals of NH stretching modes. The spectral features of the solvated clusters with proper solvent species resemble those observed in the perovskite crystal, indicating that they have similar solvation environments and hydrogen bond interactions. Therefore, a linkage between the gas-phase cluster models and the condensed-phase materials can be established, and our simulations and anharmonic analyses help in interpreting the spectral assignments of the observed IR and Raman spectra of perovskites reliably. Furthermore, we have extended this approach to the SFG spectra to demonstrate the selective appearance of bands depending on both the beam polarization configurations and the symmetry of vibrational modes.

A decomposition mechanism for Mn2(DSBDC) metal-organic frameworks in the presence of water molecules.

In this work, we investigate the effects of water on the structural stability of Mn2(DSBDC) metal-organic framework (MOF) using DFT-based calculations. It has been found that the adsorption of multiple water molecules forming a hydrogen bond network around the Mn centers plays an important role in the decomposition process. Different effects contribute to the destabilization of the MOF: water molecules that directly coordinate to the open sites displayed by a part of the Mn centers can induce a significant shift in the charge distribution as indicated by the analysis of charge density differences and the Bader charges. This adsorption process leads to a slight elongation of the metal-linker bonds. The direct interaction with the Mn center is the most stable adsorption mode for water in Mn2(DSBDC). Once these adsorption sites at the Mn centers are fully occupied, additional water molecules start to bind via hydrogen bonds to the already present water molecules or, more importantly, to the linker molecules. This, in return, leads to a significant weakening of the Mn-linker bonds, thus allowing water insertion into the Mn-linker bonds with a barrier of only 0.16 eV, which is believed to initiate the decomposition of the Mn2(DSBDC) framework. Based on a kinetic Monte Carlo model, it can be shown that high temperatures can prevent the adsorption of water molecules around the Mn sites and thus slow down the MOF decomposition.

Dipole moment enhanced π-π stacking in fluorophenylacetylenes is carried over from gas-phase dimers to crystal structures propagated through liquid like clusters.

The aggregates of monofluorinated phenylacetylenes in the gas-phase, investigated using the IR-UV double resonance spectroscopic method in combination with extensive structural search and electronic structure calculations, reveal the formation of liquid-like clusters with a π-stacked dimeric core. The structural assignment based on the IR spectra in the acetylenic and aromatic C-H stretching regions suggests that, unlike the parent non-fluorinated phenylacetylene, the substitution of a F atom on the phenyl ring increases the dipole moment, leading to robustness in the formation of a ππ stacked dimer, which propagates incorporating C-Hπ_{Ar/Ac} and C-HF interactions involving both acetylenic and aromatic C-H groups. The structural evolution of fluorophenylacetylene aggregates in the gas phase shows marginal effects due to fluorine atom position on the phenyl ring, with substitution in the para-position tending towards phenylacetylene. The present study signifies that the ππ stacked dimers act as a nucleus for the growth of higher clusters to which other molecular units are added predominantly via the {Ar}_C-Hπ_{Ar} type of interaction and the dominant interactions present in the crystal structures gradually emerge with increasing cluster size. Based on these features, gas-phase clusters of fluorophenylacetylene are hypothesized as "liquid-like clusters" acting as intermediates in the generation of various polymorphic forms starting from a ππ stacked dimer as the core molecular unit.

Collision-induced dissociation of xylose and its applications in linkage and anomericity identification.

Collision-induced dissociation (CID) of α-xylose and ß-xylose were studied using mass spectrometry and quantum chemistry calculations. Three dissociation channels, namely loss of metal ions, dehydration, and cross-ring dissociation were found. The major dissociation channel of sodium adducts is the loss of sodium ions, and the minor dissociation channels are dehydration and cross-ring dissociation. By contrast, dehydration and cross-ring dissociation are the major dissociation channels of lithium adducts, and the corresponding dissociation mechanisms can be used to determine the anomericity and linkages of xylose in oligosaccharides. These mechanisms include (1) the dehydration branching ratio can be used to differentiate the anomericity of xylose and xylose in oligosaccharides because α-xylose has a larger branching ratio of dehydration than ß-xylose, (2) various cross-ring dissociation reactions can be used to identify linkage positions. The oligosaccharide with xylose at the reducing end is predicted to undergo 0,2X, 0,3X, and 0,2A cross-ring dissociation for the 1 → 2, 1 → 3, and 1 → 4 linkages, respectively. Application of these mechanisms to determine the anomericity and linkage positions of xylobiose was demonstrated.