Hydrogen bond network structures of protonated 2,2,2-trifluoroethanol/ethanol mixed clusters probed by infrared spectroscopy combined with a deep-learning structure sampling approach: the origin of the linear type network preference in protonated fluoroalcohol clusters.

While preferential hydrogen bond network structures of cold protonated alcohol clusters H(ROH) are generally switched from a linear type to a cyclic one at = 4-5, those of protonated 2,2,2-trifluoroethanol (TFE) clusters maintain linear type structures at least in the size range of = 3-7. To explore the origin of the strong linear type network preference of H(TFE), infrared spectra of protonated mixed clusters H(TFE)(ethanol) ( + = 5) were measured. An efficient structure sampling technique using parallelized basin-hopping algorithms and deep-learning neural network potentials is developed to search for essential isomers of the mixed clusters.

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.

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 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.

Near-infrared spectroscopy of HO⋯X (X = Ar, N, and CO, = 1-3).

Near-infrared (NIR) spectra of HO⋯X (X = Ar, N, and CO, = 1-3) in the first overtone region of OH-stretching vibrations (4800-7000 cm) 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.

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 ∼10 structurally distinct conformers covering an energy range of ∼150 kJ mol. Thus, it is reasonable to expect that the number of distinct conformers for a given disaccharide would be on the order of 10. 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 compared to DFT.

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.

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

The diazenylium ion (NH) 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, ν.

Structures of (Pyrazine) 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) 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) 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.

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.

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.

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 methods is a resource intensive task due to the increasing cost of the 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 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 methods to train a deep-learning machine learning (ML) model using SchNet.

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

Collision-induced dissociation tandem mass spectrometry (CID-MS) 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 (αFru), β-fructofuranose (βFru), α-fructopyranose (αFru), and β-fructopyranose (βFru). The four isomers can be separated by high-performance liquid chromatography (HPLC) and they show different mass spectra, indicating that CID-MS 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.

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 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 in solvated aminium ions are assigned to the combination tones involving the CH-NH (methyl-amino) rocking modes.

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 (NgHNg) have a linear structure, while the protonated noble gas trimers (NgH) can have a T-shaped or linear structure. Successive binding energies for these complexes are calculated at the CCSD(T)/CBS level of theory.

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), ( = 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) 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.

Is Dissociation of HCl in DMSO Clusters Bistable?

Dissociation of HCl embedded in dimethyl sulfoxide (DMSO) clusters was investigated by projecting the solvent electric field along the HCl bond using B3LYP-D3/6-31+G(d) and MP2/6-31+G(d,p) levels of theory. A large number of distinct structures (about 1500) consisting of up to five DMSO molecules were considered in the present work for statistical reliability. The B3LYP-D3 calculations reveal that the dissociation of HCl embedded in DMSO clusters requires a critical electric field of 138 MV cm along the H-Cl bond.

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

The methylammonium ion (CHNH, 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 anharmonic algorithm at the CCSD/aug-cc-pVDZ level to simulate the IR and Raman spectra of the solvated methylammonium ion, MA-H⋯X, 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.

Structural and vibrational characterization of HCO and Rg-HCO, Rg = {He, Ne, Ar, Kr, and Xe}.

The structures of the formyl ion (HCO) and its rare gas tagged counterparts (Rg-HCO, Rg = He, Ne, Ar, Kr, and Xe) were studied at the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)]/aug-cc-pVTZ level of theory and basis set. A linear structure for these tagged complexes was predicted. The Rg binding energies for Rg-HCO are also examined at the CCSD(T) level.

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

In this work, we investigate the effects of water on the structural stability of Mn(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.

Lithium and sodium intercalation in a 2D NbSe 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 NbSe 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 VS, the structural phase transition barrier of NbSe 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.

Infrared Spectroscopy and Anharmonic Vibrational Analysis of (HO-Kr) ( = 1-3): Hemibond Formation of the Water Radical Cation.

The hemibond is a nonclassical covalent bond formed between a radical (cation) and a closed shell molecule. The hemibond formation ability of water has attracted great interest, concerning its role in ionization of water. While many computational studies on the water hemibond have been performed, clear experimental evidence has been hardly reported because the hydrogen bond formation overwhelms the hemibond formation.

Structures of Pyridine-Water Clusters Studied with Infrared-Vacuum Ultraviolet Spectroscopy.

The infrared (IR) spectra of the O-H stretching vibrations of pyridine-water clusters (Pyd)(HO), with , = 1-4, have been investigated with infrared-vacuum ultraviolet (VUV) spectroscopy under a jet-cooled condition. The time-of-flight mass spectrum of (Pyd)(HO) by VUV ionization at ∼9 eV showed an unusual intensity pattern with very weak ion signals for = 1 and 2 and stronger signals for ≥ 3. This unusual mass pattern was explained by a drastic structural change of (Pyd)(HO) upon the VUV ionization, which was followed by the elimination of water molecules.

Disentangling the Complex Vibrational Spectra of Hydrogen-Bonded Clusters of 2-Pyridone with Structural Search and Anharmonic Analysis.

Vibrational spectra of 1:1 clusters of 2-pyridone (2PY) with water, ammonia, and other hydrogen bond-forming molecules have been measured by several experimental groups over the past two decades. Complex vibrational signatures associated with the N-H stretching fundamental at 3 μm are often observed. Several anharmonic coupling schemes have been proposed; however, the origin of these commonly seen complex features remains unclear.

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.

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.