Does ammonia hydrogen bond?

Ab Initio Investigation of Tetrel Bonds in Isolated Complexes Formed Between a Lewis Acid H3MX, M-O or M-S (M = Si, Ge, or Sn) and the Lewis Bases B = N2, CO, HCCH, PH3, C2H4, HCN, CS, HNC, NP, H2O, and NH3

Isolated complexes of the type B⋯A in which the noncovalent interaction is a tetrel bond have been characterized by ab initio calculations at the CCSD(T)(F12c)/cc-pVDZ-F12 level. The Lewis bases B involved were N2, CO, HCCH, PH3, C2H4, HCN, CS, HNC, NP, H2O and NH3. Two types of Lewis acid A were examined, each containing one of the tetrel atoms M = Si, Ge or Sn, The Lewis acids in the first series were the H3MX (X = F, Cl, CN, H), in each of which the most electrophilic region was found to lie on the C3 axis of the C3v molecules, near to the tetrel atom M. In the second series the Lewis acids were M-O and M-S. Graphs, consisting of calculated equilibrium dissociation energies De of each B⋯H3MX complex plotted against the nucleophilicities NB of the Lewis bases B, were used to obtain the electrophilicity EH3MX of each molecule H3MX (M = Si, Ge, Sn). The molecular electrostatic surface of potentials of the molecules M-S and M-O (M = Si, Ge, Sn) revealed that many of the B⋯M-S and B⋯M-O complexes should have a tetrel bond to M in which the axis of the M-S or M-O subunit should be approximately perpendicular to the axis of the nonbonding or π-bonding electron pair carried by B, a novel type of tetrel bond confirmed by geometry optimizations of the complexes.

Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition

Vibrational spectroscopy allows us to understand complex physical and chemical interactions of molecular crystals and liquids such as ammonia, which has recently emerged as a strong hydrogen fuel candidate to support a sustainable society. We report inelastic neutron scattering measurement of vibrational properties of ammonia along the solid-to-liquid phase transition with high enough resolution for direct comparisons to ab-initio simulations. Theoretical analysis reveals the essential role of nuclear quantum effects (NQEs) for correctly describing the intermolecular spectrum as well as high energy intramolecular N-H stretching modes. This is achieved by training neural network models using ab-initio path-integral molecular dynamics (PIMD) simulations, thereby encompassing large spatiotemporal trajectories required to resolve low energy dynamics while retaining NQEs. Our results not only establish the role of NQEs in ammonia but also provide general computational frameworks to study complex molecular systems with NQEs.

An Exploration of the Hydrogen Bond Donor Ability of Ammonia

Ammonia is an important molecule due to its wide use in the fertiliser industry. It is also used in aminolysis reactions. Theoretical studies of the reaction mechanism predict that in reactive complexes and transition states, ammonia acts as a hydrogen bond donor forming N-H⋅⋅⋅O hydrogen bond. Experimental reports of N-H⋅⋅⋅O hydrogen bond, where ammonia acts as a hydrogen bond donor are scarce. Herein, the hydrogen bond donor ability of ammonia is investigated with three chalcogen atoms i. e. O, S, and Se using matrix isolation infrared spectroscopy and electronic structure calculations. In addition, the chalcogen bond acceptor ability of ammonia has also been investigated. The hydrogen bond acceptor molecules used here are O(CH3 )2 , S(CH3 )2 , and Se(CH3 )2 . The formation of the 1 : 1 complex has been monitored in the N-H symmetric and anti-symmetric stretching modes of ammonia. The nature of the complex has been delineated using Atoms in Molecules analysis, Natural Bond Orbital analysis, and Energy Decomposition Analysis. This work presents the first comparison of the hydrogen bond donor ability of ammonia with O, S, and Se.

Hydrogen Bonding in Liquid Ammonia

The nature of hydrogen bonding in condensed ammonia phases, liquid and crystalline ammonia has been a topic of much investigation. Here, we use quantum molecular dynamics simulations to investigate hydrogen bond structure and lifetimes in two ammonia phases: liquid ammonia and crystalline ammonia-I. Unlike liquid water, which has two covalently bonded hydrogen and two hydrogen bonds per oxygen atom, each nitrogen atom in liquid ammonia is found to have only one hydrogen bond at 2.24 Å. The computed lifetime of the hydrogen bond is t ≅ 0.1 ps. In contrast to crystalline water-ice, we find that hydrogen bonding is practically nonexistent in crystalline ammonia-I.

Ammonia dimer: extremely fluxional but still hydrogen bonded

In the 1980s, Nelson, Fraser, and Klemperer (NFK) published an experimentally derived structure of the ammonia dimer dramatically different from the structure determined computationally, which led these authors to the question "Does ammonia hydrogen bond?". This question has not yet been answered satisfactorily. To answer it, we have developed an ab initio potential energy surface (PES) for this dimer at the limits of the current computational capabilities and performed essentially exact six-dimensional calculations of the vibration-rotation-tunneling (VRT) spectra of NH₃-NH₃ and ND₃-ND₃, obtaining an unprecedented agreement with experimental spectra. In agreement with other recent electronic structure calculations, the global minimum on the PES is in a substantially bent hydrogen-bonded configuration. Since the bottom of the PES is exceptionally flat, the dimer is extremely fluxional and the probability of finding it in configurations that are not hydrogen bonded is high. Nevertheless, the probability of hydrogen-bonded configurations is large enough to consider the ammonia dimer to be hydrogen bonded. We also show that NFK's inference that the ammonia dimer is nearly rigid actually results from unusual cancellations between quantum effects that generate differences in spectra of different isotopologues.

Competition between Hydrogen Bonding and Dispersion Force in Water Adsorption and Epoxy Adhesion to Boron Nitride: From the Flat to the Curved

Hexagonal boron nitride (h-BN) is a material with excellent thermal conductivity and electrical insulation, used as an additive to various matrices. To increase the affinity of h-BN to them, hydrogen bonds should be formed at the interface. In reality, however, they are not formed; the N atoms are not capable of accepting hydrogen bonds due to the delocalization of their lone pair electrons over the B-N π bonds. To make it form hydrogen bonds, one may need to break the planarity of h-BN so that the orbital overlap in the B-N π bonds can be reduced. This idea is verified with first-principles calculations on the adsorption of a water molecule on hypothetical h-BN surfaces, the planarity of which is broken. One can do it in silico but not in vitro. BN nanotubes (BNNTs) are considered as a more realistic BN surface with nonplanarity. The hydrogen bond is shown to become stronger as the curvature of the tube increases. On the contrary, the strength of the dispersion force acting at the interface becomes weaker. In water adsorption, these two interactions are in competition with each other. However, in epoxy adhesion, the interaction due to dispersion forces is overwhelmingly stronger than that due to hydrogen bonding. The smaller the curvature of the surface, the smaller the distance between more atoms at the interface; thus, the interaction due to dispersion forces maximized.

Coordination of a Neutral Ligand to a Metal Center of Oxohalido Anions: Fact or Fiction?

Can a neutral ligand bond to a metal center of a square pyramidal oxohalido anion at the available sixth octahedral position? Crystal structures of some compounds indeed suggest that ligands, such as THF, pyridine, H₂O, NH₃, and CH₃CN, can interact with the central metal atom, because they are oriented with their heteroatom toward the metal center with distances being within the bonding range. However, this assumption that is based on chemical intuition is wrong. In-depth analysis of interactions between ligands and oxohalido anions (e.g., VOX₄^–, NbOCl₄^–) reveals that the bonding of a neutral ligand is almost entirely due to electrostatic interactions between the H atoms of a ligand and halido atoms of an anion. Furthermore, ab initio calculations indicate that the ligand–VOF₄^– interactions represent only about one-quarter of the total binding of the ligand within the crystal structure, whereas the remaining binding is due to crystal packing effects. The current study therefore shows that relying solely on the structural aspects of solved crystal structures, such as ligand orientation and bond distances, can lead to the wrong interpretation of the chemical bonding.

Some crystal structures suggest that ligands interact chemically with the metal center of oxohalido anions. However, analysis shows that the attraction between the heteroatom of the ligand and the metal center is counteracted by the repulsion between the heteroatom and the electronegative F atoms, making electrostatic F···H interactions and crystal packing effects the dominant force holding the ligand and anion together. This is the reason why some ligands rotate with their heteroatom away from the metal center.

Intermolecular dynamics of NH3-rare gas complexes in the ν2 umbrella region of NH3 investigated by rovibrational laser jet-cooled spectroscopy and ab initio calculations

High resolution jet-cooled spectroscopy experiments have been realized to investigate the intermolecular dynamics of van der Waals (vdW) heterodimers between NH₃ and rare gas (Rg) atoms in the ν₂ umbrella mode region of NH₃. With respect to a previous study dedicated to NH₃-Ar [Asselin et al. Mol. Phys. 116, 3642 (2018)], the sensitivity and spectral resolution of our laser spectrometer coupled to a pulsed supersonic jet have been significantly improved to derive more accurate excited state spectroscopic parameters from rovibrational analyses. In addition, we calculated the ground and ν₂ excited vibration-rotation-tunneling (VRT) states of these complexes on the four-dimensional ab initio potential energy surfaces from Loreau et al. [J. Chem. Phys. 141, 224303 (2014), ibid. 143, 184303 (2015).] Transition frequencies and intensities of the allowed ν₂ = 1 ← 0 transitions obtained from the calculated energy levels and wave functions agree well with the experimental data and are helpful in their analysis. By means of a pseudodiatomic model with the assumption of weak Coriolis coupling, the rovibrational analysis of both the Π_e/f(j = 1,k = 0) ←Σ_f(j = 0,k = 0) and Σ_f(j = 1,k = 0) ←Σ_f(j = 0,k = 0) transitions in ortho NH₃-Rg (Rg = Ne, Ar, Kr, Xe) complexes enabled us to determine reliable excited state parameters and derive accurate values of the effective vdW bond length R_eff, force constant k_s, and vdW stretching frequency ν_s. Comparison between the experimental structural parameters and those from the ab initio calculated VRT levels shows good agreement for NH₃-Ne, NH₃-Ar and NH₃-Kr, and a similar variation of R_eff, k_s, and ν_s with the polarizability of Rg in the ground and ν₂ excited states. Anomalously small values of ν_s and k_s derived for NH₃-Xe in the Π_e/f(j = 1,k = 0) state suggest that the applied model is not valid in this case, due to the presence of another state coupling to the perturbed Π_f state. Such a state could not be found, however.

Characterizing the lone pair⋯π–hole interaction in complexes of ammonia with perfluorinated arenes

Stronger and more flexible lone pair⋯π–hole interaction of ammonia with respect to water in complexes with perfluorinated arenes.

Nucleophilic Aromatic Substitution of Unactivated Fluoroarenes Enabled by Organic Photoredox Catalysis

Nucleophilic aromatic substitution (SNAr) is a classical reaction with well-known reactivity toward electron-poor fluoroarenes. However, electron-neutral and electron-rich fluoro(hetero)arenes are considerably underrepresented. Herein, we present a method for the nucleophilic defluorination of unactivated fluoroarenes enabled by cation radical-accelerated nucleophilic aromatic substitution. The use of organic photoredox catalysis renders this method operationally simple under mild conditions and is amenable to various nucleophile classes, including azoles, amines, and carboxylic acids. Select fluorinated heterocycles can be functionalized using this method. In addition, the late-stage functionalization of pharmaceuticals is also presented. Computational studies demonstrate that the site selectivity of the reaction is dictated by arene electronics.

Chloride ions as integral parts of hydrogen bonded networks in aqueous salt solutions: the appearance of solvent separated anion pairs

Characteristic hydrogen bonded motifs, including solvent separated anion pairs, in concentrated aqueous LiCl solutions.

Aqueous Solvation of Ammonia and Ammonium: Probing Hydrogen Bond Motifs with FT-IR and Soft X-ray Spectroscopy

In a multifaceted investigation combining local soft X-ray and vibrational spectroscopic probes with ab initio molecular dynamics simulations, hydrogen-bonding interactions of two key principal amine compounds in aqueous solution, ammonia (NH₃) and ammonium ion (NH₄⁺), are quantitatively assessed in terms of electronic structure, solvation structure, and dynamics. From the X-ray measurements and complementary determination of the IR-active hydrogen stretching and bending modes of NH₃ and NH₄⁺ in aqueous solution, the picture emerges of a comparatively strongly hydrogen-bonded NH₄⁺ ion via N-H donating interactions, whereas NH₃ has a strongly accepting hydrogen bond with one water molecule at the nitrogen lone pair but only weakly N-H donating hydrogen bonds. In contrast to the case of hydrogen bonding among solvent water molecules, we find that energy mismatch between occupied orbitals of both the solutes NH₃ and NH₄⁺ and the surrounding water prevents strong mixing between orbitals upon hydrogen bonding and, thus, inhibits substantial charge transfer between solute and solvent. A close inspection of the calculated unoccupied molecular orbitals, in conjunction with experimentally measured N K-edge absorption spectra, reveals the different nature of the electronic structural effects of these two key principal amine compounds imposed by hydrogen bonding to water, where a pH-dependent excitation energy appears to be an intrinsic property. These results provide a benchmark for hydrogen bonding of other nitrogen-containing acids and bases.

Nonadiabatic dynamics of floppy hydrogen bonded complexes: the case of the ionized ammonia dimer

Non-adiabatic dynamics of a floppy hydrogen bonded ammonia dimer was studied by ab initio molecular dynamics simulations.

Micelle Formation in Liquid Ammonia

Perfluorinated long chain alkyl amides aggregate in liquid ammonia with increasing concentration which reflects micelle-type formation based on changes in (19)F NMR chemical shifts. The critical micelle concentrations (cmc) decrease with increasing chain length and give Kleven parameters A = 0.18 and B = 0.19. The micelles catalyze the ammonolysis of esters in liquid ammonia. The corresponding perfluorinated long chain alkyl carboxylates form ion pairs in liquid ammonia, but the equilibrium dissociation constants indicate favorable interactions between the chains in addition to the electrostatic forces. These perfluorinated carboxylates form micelles in aqueous solution, and their cmc's generate a Kleven B-value = 0.52 compared with 0.30 for the analogous alkyl carboxylates. The differences in hydrophobicity of CH2 and CF2 units in water and liquid ammonia are discussed, as is the possible relevance to life forms in liquid ammonia.

Fourier transform infrared spectroscopy and theoretical study of dimethylamine dimer in the gas phase

Dimethylamine (DMA) has been studied by gas-phase Fourier transform infrared (FTIR) spectroscopy. We have identified a spectral transition that is assigned to the DMA dimer. The IR spectra of the dimer in the gas phase are obtained by spectral subtraction of spectra recorded at different pressures. The enthalpy of hydrogen bond formation was obtained for the DMA dimer by temperature-dependence measurements. We complement the experimental results with ab initio and anharmonic local mode model calculations of monomer and dimer. Compared to the monomer, our calculations show that in the dimer the N-H bond is elongated, and the NH-stretching fundamental shifts to a lower wavenumber. More importantly, the weak NH-stretching fundamental transition has a pronounced intensity increase upon complexation. However, the first NH-stretching overtone transition is not favored by the same intensity enhancement, and we do not observe the first NH-stretching overtone of the dimer. On the basis of the measured and calculated intensity of the NH-stretching transition of the dimer, the equilibrium constant for dimerization at room temperature was determined.

Highly compressed ammonia forms an ionic crystal

Ammonia is an important compound with many uses, such as in the manufacture of fertilizers, explosives and pharmaceuticals. As an archetypal hydrogen-bonded system, the properties of ammonia under pressure are of fundamental interest, and compressed ammonia has a significant role in planetary physics. We predict new high-pressure crystalline phases of ammonia (NH(3)) through a computational search based on first-principles density-functional-theory calculations. Ammonia is known to form hydrogen-bonded solids, but we predict that at higher pressures it will form ammonium amide ionic solids consisting of alternate layers of NH(4)(+) and NH(2)(-) ions. These ionic phases are predicted to be stable over a wide range of pressures readily obtainable in laboratory experiments. The occurrence of ionic phases is rationalized in terms of the relative ease of forming ammonium and amide ions from ammonia molecules, and the volume reduction on doing so. We also predict that the ionic bonding cannot be sustained under extreme compression and that, at pressures beyond the reach of current static-loading experiments, ammonia will return to hydrogen-bonded structures consisting of neutral NH(3) molecules.

Spectral-luminescent properties of 12-oximino derivatives of 8-AZA-D-homogona-12,17a-diones and their concentration dependence

This paper presents the results of the investigation of the spectral-luminescent characteristics of 12-oximino derivative of 8-aza-D-homogona-12,17a-dion, its hydrochloride, and their dependences on the concentration. It has been shown that the form and position of the absorption spectrums of 16,16-dimethyl-12-oximino-8-aza-D-homogona-1,3,5(10),13-tetraene-17a-one in all solvents used are independent of its concentration. At the same time, for its hydrochloride in ethanol and water, a strong dependence of the absorption spectrum on its concentration has been revealed. On the basis of the experimental data it has been concluded that in these solvents dimers of investigated substance, whose bonding force is chelate hydrogen bonds, are formed. The investigation of the luminescence has shown that these substances practically do not fluoresce. Only in ethanol and water we managed to register a very weak luminescence, whose excitation spectrum is close to the absorption spectrum.

Study of NH Stretching Vibrations in Small Ammonia Clusters by Infrared Spectroscopy in He Droplets and ab Initio Calculations†

Infrared spectra of the NH stretching vibrations of (NH3)n clusters (n = 2-4) have been obtained using the helium droplet isolation technique and first principles electronic structure anharmonic calculations. The measured spectra exhibit well-resolved bands, which have been assigned to the nu1, nu3, and 2nu4 modes of the ammonia fragments in the clusters. The formation of a hydrogen bond in ammonia dimers leads to an increase of the infrared intensity by about a factor of 4. In the larger clusters the infrared intensity per hydrogen bond is close to that found in dimers and approaches the value in the NH3 crystal. The intensity of the 2nu4 overtone band in the trimer and tetramer increases by a factor of 10 relative to that in the monomer and dimer, and is comparable to the intensity of the nu1 and nu3 fundamental bands in larger clusters. This indicates the onset of the strong anharmonic coupling of the 2nu4 and nu1 modes in larger clusters. The experimental assignments are compared to the ones obtained from first principles electronic structure anharmonic calculations for the dimer and trimer clusters. The anharmonic calculations were performed at the Møller-Plesset (MP2) level of electronic structure theory and were based on a second-order perturbative evaluation of rovibrational parameters and their effects on the vibrational spectra and average structures. In general, there is excellent (<20 cm(-1)) agreement between the experimentally measured band origins for the N-H stretching frequencies and the calculated anharmonic vibrational frequencies. However, the calculations were found to overestimate the infrared intensities in clusters by about a factor of 4.

Dynamics and fragmentation of van der Waals clusters: (H2O)n, (CH3OH)n, and (NH3)n upon ionization by a 26.5eV soft x-ray laser

A tabletop soft x-ray laser is applied for the first time as a high energy photon source for chemical dynamics experiments in the study of water, methanol, and ammonia clusters through time of flight mass spectroscopy. The 26.5 eV/photon laser (pulse time duration of approximately 1 ns) is employed as a single photon ionization source for the detection of these clusters. Only a small fraction of the photon energy is deposited in the cluster for metastable dissociation of cluster ions, and most of it is removed by the ejected electron. Protonated water, methanol, and ammonia clusters dominate the cluster mass spectra. Unprotonated ammonia clusters are observed in the protonated cluster ion size range 2< or =n< or =22. The unimolecular dissociation rate constants for reactions involving loss of one neutral molecule are calculated to be (0.6-2.7)x10(4), (3.6-6.0)x10(3), and (0.8-2.0)x10(4) s(-1) for the protonated water (9< or =n< or =24), methanol (5< or =n< or =10), and ammonia (5< or =n< or =18) clusters, respectively. The temperatures of the neutral clusters are estimated to be between 40 and 200 K for water clusters (10< or =n< or =21), and 50-100 K for methanol clusters (6< or =n< or =10). Products with losses of up to five H atoms are observed in the mass spectrum of the neutral ammonia dimer. Large ammonia clusters (NH(3))(n) (n>3) do not lose more than three H atoms in the photoionization/photodissociation process. For all three cluster systems studied, single photon ionization with a 26.5 eV photon yields near threshold ionization. The temperature of these three cluster systems increases with increasing cluster size over the above-indicated ranges.

Terahertz Vibration−Rotation-Tunneling Spectroscopy of the Ammonia Dimer: Characterization of an out of Plane Vibration

The terahertz vibration-rotation-tunneling (VRT) spectrum of the ammonia dimer (NH(3))(2) has been measured between ca. 78.5 and 91.9 cm(-1). The dipole-allowed transitions are separated into three groups that correspond to the 3-fold internal rotation of the NH(3) subunits. Transitions have been assigned for VRT states of the A-A (ortho-ortho) combinations of NH(3) monomer states. The spectrum is further complicated by strong Coriolis interactions. K = 0 <-- 0, K = 1 <-- 0, K = 0 <-- 1, and K = 1 <-- 1 progressions have been assigned. The band origins, rotational constants, asymmetry doubling, centrifugal distortion, and Coriolis coupling constant have been determined from the fit to an effective Hamiltonian. These VRT transitions are tentatively assigned to an out of plane vibration with a K = 0 state at 89.141305(47) cm(-1), and a K = 1 state at 86.77785(9) cm(-1).

On the Surface-Catalyzed Reaction between the Gases 2,2-Dimethylpropanal and Methanamine. Formation of Active-Site Imines

The reaction that occurs when vapors of 2,2-dimethylpropanal and methanamine are allowed to mix in an infrared gas cell has been examined. The disappearance of starting materials and formation of E-imine product, monitored simultaneously, is best fit by a process involving wall-associated water. The same or closely related processes have been successfully modeled; such processes may also be common to pyridoxal-catalyzed transamination and related reactions in biological systems.

Synthesis of 3'-deoxy-3'-difluoromethyl azanucleosides from trans-4-hydroxy-l-proline

[reaction: see text] Two strategies were tried to synthesize 3'-deoxy-3'-difluoromethyl azanucleosides. After the failure of the first route, the key intermediate 12 from trans-4-hydroxyproline 7 in 8 steps was stereoselectively prepared. The alcohol 12 was subjected to selective protection, oxidation, and difluoromethylenation to afford the fluorinated compound 18, whose hydrogenation was then systematically investigated. After a series of transformations of protecting groups, the resultant compounds 22 and 23 were oxidized to the desired lactams 24 and 25, which were successfully utilized to synthesize our target molecules, 3'-deoxy-3'-difluoromethyl azanucleosides 33, 34a, 34b, and 35.