The equilibrium OH bond length

Equilibrium Structures of Propane and 2,2-Difluoropropane and Comparison with Other Two-Top Molecules

The Born-Oppenheimer ab initio equilibrium structures of propane (CH3)2CH2 and 2,2-difluoropropane (CH3)2CF2 were computed at the CCSD(T) level of theory using a basis set of quadruple zeta quality. The semiexperimental structure of propane was also determined from the ground state rotational constants corrected for rovibrational corrections calculated at the MP2 level of theory. Structural comparisons are made with other molecules and are discussed in terms of the quantum theory of atoms in molecules.

Calculated vibration spectrum of calcium hexahydroxodizincate dihydrate (qatranaite)

On the basis of first-principles electronic structure calculations, crystallographic parameters have been refined for calcium hydroxozincate (Qatranaite mineral), and the vibration properties (frequencies and eigenvectors) calculated. A detailed analysis of vibration modes is done, in the context of comparison with infrared and Raman spectra previously available. Special attention is paid to a posteriori symmetry analysis of vibration modes, discussing the latters' attribution to four irreducible representations of the P21/c space group, and to identifying stretchings and bendings of particular chemical bonds, pronounced in different vibrations. It turns out that high-frequency (>700 cm-1) vibrations of hydroxyl groups bridging the Ca or Zn cations differ quite considerably for crystallographically distinct hydroxyl positions. It is shown that the vibrations involving hydroxyl groups and crystalline water typically come about in quadruplets at very close frequencies, whereby different irreducible representations reflect different combinations of similar "molecular" vibrations of four identical entities (of each hydroxyl or water) present in the unit cell. However, some vibrations show exceptions from this rule. In addition to interpretation of earlier experimental investigations, our study indicates that the low-frequency (<700 cm-1) vibrations within the cation-hydroxyl connected skeleton are of more "solid-state-like" character and cannot be reasonably interpreted in terms of "molecular" vibrations within ZnO4 or CaO6 units.

Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation

This work introduces a new faster implementation of the hydrogen bond network (complex arrangement of hydrogen bonds between or within molecules) search algorithm in biomacromolecules and their environment. Existing implementation of such an algorithm in GROMACS [Abraham et al. GROMACS 2024.2 Manual. 2024.] has limitations in the analysis of large structures and trajectories. The new implementation, in the form of a native GROMACS trajectory analysis module, allows for quick analysis of molecular dynamics trajectories without restrictions, thus overcoming the limitations of the original algorithm. The application of the developed method enabled the acquisition and analysis of hydrogen bond networks in the studied defensin-like protein Pentadiplandra brazzeana, as well as the study of hydrogen bond occupancies between the protein's residues and water molecules. The data obtained using the new implementation coincided with the experimental data.

Fragment-based models for dissociation of strong acids in water: Electrostatic embedding minimizes the dependence on the fragmentation schemes

Fragmentation methods such as MIM (Molecules-in-Molecules) provide a route to accurately model large systems and have been successful in predicting their structures, energies, and spectroscopic properties. However, their use is often limited to systems at equilibrium due to the inherent complications in the choice of fragments in systems away from equilibrium. Furthermore, the presence of charges resulting from any heterolytic bond breaking may increase the fragmentation error. We have previously suggested EE-MIM (Electrostatically Embedded Molecules-In-Molecules) as a method to mitigate the errors resulting from the missing long-range interactions in molecular clusters in equilibrium. Here, we show that the same method can be applied to improve the performance of MIM to solve the longstanding problem of dependency of the fragmentation energy error on the choice of the fragmentation scheme. We chose four widely used acid dissociation reactions (HCl, HClO4, HNO3, and H2SO4) as test cases due to their importance in chemical processes and complex reaction potential energy surfaces. Electrostatic embedding improves the performance at both one and two-layer MIM as shown by lower EE-MIM1 and EE-MIM2 errors. The EE-MIM errors are also demonstrated to be less dependent on the choice of the fragmentation scheme by analyzing the variation in fragmentation energy at the points with more than one possible fragmentation scheme (points where the fragmentation scheme changes). EE-MIM2 with M06-2X as the low-level resulted in a variation of less than 1 kcal/mol for all the cases and 1 kJ/mol for all but three cases, rendering our method fragmentation scheme-independent for acid dissociation processes.

Syntheses, Structures, and Corrosion Inhibition of Various Alkali Metal Carboxylate Complexes

Complexes of the alkali metals Li-Cs with 3-thiophenecarboxylate (3tpc), 2-methyl-3-furoate (2m3fur), 3-furoate (3fur), 4-hydroxycinnamate (4hocin), and 4-hydroxybenzoate (4hob) ions were prepared via neutralisation reactions, and the structures of [Li₂(3tpc)₂]_n (1Li); [K₂(3tpc)₂]_n (1K); [Rb(3tpc)(H₂O)]_n (1Rb); [Cs{H(3tpc)₂}]_n (1Cs); [Li₂(2m3fur)₂(H₂O)₃] (2Li); [K₂(2m3fur)₂(H₂O)]_n (2K); [Li(3fur)]_n(3Li); [K(4hocin](H₂O)₃]_n (4K); [Rb{H(4hocin)₂}]_n.nH₂O (4Rb); [Cs(4hocin)(H₂O)]_n (4Cs); [Li(4hob)]_n (5Li); [K(4hob)(H₂O)₃]_n (5K); [Rb(4hob)(H₂O)]_n (5Rb); and [Cs(4hob)(H₂O)]_n (5Cs) were determined via X-ray crystallography. Bulk products were also characterised via XPD, IR, and TGA measurements. No sodium derivatives could be obtained as crystallographically suitable single crystals. All were obtained as coordination polymers with a wide variety of carboxylate-binding modes, except for dinuclear 2Li. Under conditions that normally gave coordinated carboxylate ions, the ligation of hydrogen dicarboxylate ions was observed in 1Cs and 4Rb, with short H-bonds and short O…O distances associated with the acidic hydrogen. The alkali-metal carboxylates showed corrosion inhibitor properties inferior to those of the corresponding rare-earth carboxylates.

The Adsorption Mechanism of Hydrogen on FeO Crystal Surfaces: A Density Functional Theory Study

The hydrogen-based direct reduction of iron ores is a disruptive routine used to mitigate the large amount of CO₂ emissions produced by the steel industry. The reduction of iron oxides by H₂ involves a variety of physicochemical phenomena from macroscopic to atomistic scales. Particularly at the atomistic scale, the underlying mechanisms of the interaction of hydrogen and iron oxides is not yet fully understood. In this study, density functional theory (DFT) was employed to investigate the adsorption behavior of hydrogen atoms and H₂ on different crystal FeO surfaces to gain a fundamental understanding of the associated interfacial adsorption mechanisms. It was found that H₂ molecules tend to be physically adsorbed on the top site of Fe atoms, while Fe atoms on the FeO surface act as active sites to catalyze H₂ dissociation. The dissociated H atoms were found to prefer to be chemically bonded with surface O atoms. These results provide a new insight into the catalytic effect of the studied FeO surfaces, by showing that both Fe (catalytic site) and O (binding site) atoms contribute to the interaction between H₂ and FeO surfaces.

Hybrid G/BN@2H-MoS2 Nanomaterial Composites: Structural, Electronic and Molecular Adsorption Properties

Hybrid structures often possess superior properties to those of their component materials. This arises from changes in the structural or physical properties of the new materials. Here, we investigate the structural, electronic, and gas-adsorption properties of hybrid structures made from graphene/hexagonal boron nitride and 2H-molybdenum disulfide (G/BN@MoS₂) monolayers. We consider hybrid systems in which the G/BN patch is at the Mo plane (model I) and the S plane (model II). We find that the implanted hexagon of G or BN in MoS₂ alters its electronic properties: G@MoS₂ (I,II) are metallic, while BN@MoS₂ (I) is an n-type conducting and BN@MoS₂ (II) is semiconducting. We study the molecular adsorption of some diatomic gases (H₂, OH, N₂, NO, CO), triatomic gases (CO₂, NO₂, H₂S, SO₂), and polyatomic gases (COOH, CH₄, and NH₃) on our hybrid structures while considering multiple initial adsorption sites. Our results suggest that the hybrid systems may be suitable materials for some applications: G@MOS₂ (I) for oxygen reduction reactions, BN@MoS₂ (I,II) for NH₃-based hydrogen production, and G@MoS₂ (I) and BN@MoS₂ (I,II) for filtration of No, Co, SO₂, H₂S, and NO₂.

Influence of water contamination on the sputtering of silicon with low-energy argon ions investigated by molecular dynamics simulations

Focused ion beams (FIB) are a common tool in nanotechnology for surface analysis, sample preparation for electron microscopy and atom probe tomography, surface patterning, nanolithography, nanomachining, and nanoprinting. For many of these applications, a precise control of ion-beam-induced processes is essential. The effect of contaminations on these processes has not been thoroughly explored but can often be substantial, especially for ultralow impact energies in the sub-keV range. In this paper we investigate by molecular dynamics (MD) simulations how one of the most commonly found residual contaminations in vacuum chambers (i.e., water adsorbed on a silicon surface) influences sputtering by 100 eV argon ions. The incidence angle was changed from normal incidence to close to grazing incidence. For the simulation conditions used in this work, the adsorption of water favours the formation of defects in silicon by mixing hydrogen and oxygen atoms into the substrate. The sputtering yield of silicon is not significantly changed by the contamination, but the fraction of hydrogen and oxygen atoms that is sputtered largely depends on the incidence angle. This fraction is the largest for incidence angles between 70 and 80° defined with respect to the sample surface. Overall, it changes from 25% to 65%.

Hybrid MXene-Graphene/Hexagonal Boron Nitride Structures: Electronic and Molecular Adsorption Properties

Recent advances in experimental techniques allow for the fabrication of hybrid structures. Here, we study the electronic and molecular adsorption properties of the graphene (G)/hexagonal boron nitride (h-BN)-MXenes (Mo2C) hybrid nanosheets. We use first-principles calculations to explore the structure and electronic properties of the hybrid structures of G-2H-Mo2C and h-BN-2H-Mo2C with two different oxygen terminations of the Mo2C surface. The embedding of G or h-BN patches creates structural defects at the patch-Mo2C border and adds new states in the vicinity of the Fermi energy. Since this can be utilized for molecular adsorption and/or sensing, we investigate the ability of the G-M-O1 and BN-M-O1 hybrid structures to adsorb twelve molecules. Generally, the adsorption on the hybrid systems is significantly higher than on the pristine systems, except for N2 and H2, which are weakly adsorbed on all systems. We find that OH, NO, NO2, and SO2 are chemisorbed on the hybrid systems. COOH may be chemisorbed, or it may dissociate depending on its location at the edge between the G/h-BN and the MXene. NH3 is chemisorbed/physisorbed on the BN/G-M-O1 systems. CO, H2S, CO2, and CH4 are physisorbed on the hybrid systems. Our results indicate that the studied hybrid systems can be used for molecular filtration/sensing and catalysis.

Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry

The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical–chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of the role played by dynamical and environmental effects in tuning their overall behavior. For small semi-rigid systems in the gas phase, state-of-the-art quantum chemical computations rival the most sophisticated experimental (from, for example, high-resolution spectroscopy) results. For larger molecules, more effective computational approaches must be devised. To this end, we have further enlarged the compilation of available semi-experimental (SE) equilibrium structures, now covering the most important fragments containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new SE100 database. Next, comparison with geometries optimized by methods rooted in the density functional theory showed that the already remarkable results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals can be further improved by a linear regression (LR) approach. Use of template fragments (taken from the SE100 library) together with LR estimates for the missing interfragment parameters paves the route toward accurate structures of large molecules, as witnessed by the very small deviations between computed and experimental rotational constants. The whole approach has been implemented in a user-friendly tool, termed nano-LEGO, and applied to a number of demanding case studies.

A New Solid-State Proton Conductor: The Salt Hydrate Based on Imidazolium and 12-Tungstophosphate

We report the structure and charge transport properties of a novel solid-state proton conductor obtained by acid–base chemistry via proton transfer from 12-tungstophosphoric acid to imidazole. The resulting material (henceforth named Imid₃WP) is a solid salt hydrate that, at room temperature, includes four water molecules per structural unit. To our knowledge, this is the first attempt to tune the properties of a heteropolyacid-based solid-state proton conductor by means of a mixture of water and imidazole, interpolating between water-based and ionic liquid-based proton conductors of high thermal and electrochemical stability. The proton conductivity of Imid₃WP·4H₂O measured at truly anhydrous conditions reads 0.8 × 10^–6 S cm^–1 at 322 K, which is higher than the conductivity reported for any other related salt hydrate, despite the lower hydration. In the pseudoanhydrous state, that is, for Imid₃WP·2H₂O, the proton conductivity is still remarkable and, judging from the low activation energy (E_a = 0.26 eV), attributed to structural diffusion of protons. From complementary X-ray diffraction data, vibrational spectroscopy, and solid-state NMR experiments, the local structure of this salt hydrate was resolved, with imidazolium cations preferably orienting flat on the surface of the tungstophosphate anions, thus achieving a densely packed solid material, and water molecules of hydration that establish extremely strong hydrogen bonds. Computational results confirm these structural details and also evidence that the path of lowest energy for the proton transfer involves primarily imidazole and water molecules, while the proximate Keggin anion contributes with reducing the energy barrier for this particular pathway.

Thermodynamic Characterization of Free and Surface Water of Colloidal Unimolecular Polymer (CUP) Particles Utilizing DSC

Colloidal Unimolecular Polymer (CUP) particles are spheroidal, 3–9 nm with charged groups on the surface and a hydrophobic core, which offer a larger surface water fraction to improve the analysis of its characteristics. Differential scanning calorimetry (DSC) was performed to determine the characteristics of surface water. These properties include the amount of surface water, the layer thickness, density, specific heat of the surface water above and below the freezing point of water, melting point depression of free water, effect of charge density and particle size. The charge density on the CUP surface was varied as well as the molecular weight which controls the particle diameter. The surface water is proportional to the weight fraction of CUP <20%. Analogous to recrystallization the CUP particles were trapped in the ice when rapidly cooled but slow cooling excluded the CUP, causing inter-molecular counterion condensation and less surface water. The density of surface water was calculated to be 1.023 g/mL to 1.056 g/mL depending on the surface charge density. The thickness of surface water increased with surface charge density. The specific heat of surface water was found to be 3.04 to 3.07 J/g·K at 253.15 K and 3.07 to 3.09 J/g·K at 293.15 K. The average area occupied by carboxylate and ester groups on the CUP surface were determined.

Tunable bending modulus and bending limit of oxidized graphene

Graphene is highly flexible and widely used in flexible devices. However, is the oxidized graphene more flexible than graphene? This is still under debate between simulations and experiments. By employing density functional theory calculations, we show that the bending modulus of oxidized graphene is quite tunable by changing the type and coverage of the functional groups, as well as the bending direction. The hydroxyl increases the bending modulus of graphene, but epoxide can degrade the bending modulus in the armchair bending direction, making the oxidized graphene more flexible than graphene. On the other hand, there exists a curvature limit during bending the oxidized graphene, where OH hydrogen bonds start to transform into O-H covalent bonds. Generally, our results demonstrate the effects of the functional groups and bending direction on the flexibility of oxidized graphene, which should be helpful to design graphene-based flexible devices.

Small Alcohols Revisited: CCSD(T) Relative Potential Energies for the Minima, First- and Second-Order Saddle Points, and Torsion-Coupled Surfaces

The elucidation of conformations and relative potential energies (rPEs) of small molecules has a long history across a diverse range of fields. Periodically, it is helpful to revisit what conformations have been investigated and to provide a consistent theoretical framework for which clear comparisons can be made. In this paper, we compute the minima, first- and second-order saddle points, and torsion-coupled surfaces for methanol, ethanol, propan-2-ol, and propanol using consistent high-level MP2 and CCSD(T) methods. While for certain molecules more rigorous methods were employed, the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pV5Z theory level was used throughout to provide relative energies of all minima and first-order saddle points. The rPE surfaces were uniformly computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ level. To the best of our knowledge, this represents the most extensive study for alcohols of this kind, revealing some new aspects. Especially for propanol, we report several new conformations that were previously not investigated. Moreover, two metrics are included in our analysis that quantify how the selected surfaces are similar to one another and hence improve our understanding of the relationship between these alcohols.

The equilibrium molecular structures of 2-deoxyribose and fructose by the semiexperimental mixed estimation method and coupled-cluster computations

The mixed estimation method yields very accurate equilibrium structures, as observed in deoxyribose and fructose.

Interplay of experiment and theory: high resolution infrared spectrum and accurate equilibrium structure of BF2OH

Substitution of hydrogen by deuterium induces a large rotation of the principal axis system that amplifies the errors.

The structure of H2TiO3—a short discussion on “Lithium recovery from salt lake brine by H2TiO3”

The phase of H₂TiO₃ prepared by treating Li₂TiO₃ with HCl is not monoclinic.