Cooperativity between Intermolecular Hydrogen and Carbon Bonds in ZY···CH3CN/CH3NC···HX Trimers (ZY = H2O, H2S, HF, HCl, HBr, NH3, and H2CO; HX = HF, HCl, and HBr).

Hydrogen-bonding and carbon-bonding interactions are widespread in nature. We studied the cooperativity between these interactions in 42 trimeric complexes ZY···CH3CN/CH3NC···HX, where ZY molecules are H2O, H2S, HF, HCl, HBr, NH3, and H2CO, and HX molecules are HF, HCl, and HBr. Acetonitrile (CH3CN) and isoacetonitrile (CH3NC) act as hydrogen bond acceptors as well as carbon bond donors in these trimers. Various theoretical methods, such as electronic structure calculations, quantum theory of atoms in molecule (QTAIM), natural bond orbital (NBO), and reduced density gradient analysis, are employed to study these trimers, and the results are compared with the corresponding ZY···CH3CN/CH3NC and CH3CN/CH3NC···HX dimers. Electronic structure calculations are performed at the second-order MoÌ·ller-Plesset perturbation theory using the 6-311++G(2d,2p) basis set. We show that both the interactions act synergistically in these trimers leading to an increase in their bond strength as compared to the strength in the individual dimers. The cooperative energies for these trimers are in the range of 0.69 to 3.22 kJ/mol. It is seen that the carbon bonds benefit more from the cooperativity than the hydrogen bonds. The trends of cooperativity and correlations of interaction energies and cooperative energies with relevant QTAIM and NBO parameters are reported.

Internal Electric Field-Induced Formation of Exotic Linear Acetonitrile Chains.

The application of external electric and magnetic fields is a powerful tool for aligning molecules in a controlled way, if the thermal fluctuations are small. Here we demonstrate that the same holds for internal electric fields in a molecular cluster. The electric field of a single molecular dipole, HCl, is used to manipulate the aggregation mechanism of subsequently added acetonitrile molecules. As a result, we could form exotic linear acetonitrile (CH3CN) chains at 0.37 K, as confirmed by infrared spectroscopy in superfluid helium nanodroplets. These linear chains are not observed in the absence of HCl and can be observed only when the internal electric field created by an HCl molecule is present. The accompanying simulations provide mechanistic insights into steric control, explain the selectivity of the process, and show that non-additive electronic polarization effects systematically enhance the dipole moment of these linear chains. Thus, adding more CH3CN monomers even supports further quasi-linear chain growth.

Zwitter Ionization of Glycine at Outer Space Conditions due to Microhydration by Six Water Molecules.

We investigate glycine microsolvation with water molecules, mimicking astrophysical conditions, in our laboratory by embedding these clusters in helium nanodroplets at 0.37 K. We recorded mass selective infrared spectra in the frequency range 1500-1800 cm^{-1} where two bands centered at 1630 and 1724 cm^{-1} were observed. By comparison with the extensive accompanying calculations, the band at 1630 cm^{-1} was assigned to the COO^{-} asymmetric stretching mode of the zwitter ion and the band at 1724 cm^{-1} was assigned to redshifted C=O stretch within neutral clusters. We show that zwitter ion formation of amino acids readily occurs with only few water molecules available even under extreme conditions.

An infrared spectroscopic study of trifluoromethoxybenzene⋯methanol complexes formed in superfluid helium nanodroplets.

We have studied the intermolecular complex formation between trifluoromethoxybenzene and methanol (CD3OD) in superfluid helium droplets by infrared spectroscopy in the spectral range of 2630-2730 cm-1, covering the O-D stretches of methanol-d4 (CD3OD). The cluster size associated with the observed bands is deduced from the variation of infrared intensity of a particular band with the partial pressures of trifluoromethoxybenzene and methanol. Quantum chemical calculations are performed at the MP2/6-311++G(d,p) level of theory to complement the experimental results. As a result, we have identified six different conformers of the trifluoromethoxybenzene⋯methanol intermolecular complex: three bound via O-H⋯O hydrogen bonds and the other three via O-H⋯π hydrogen bonds. Furthermore, to access the effect of fluorination on the methyl unit of anisole molecules, we compare the IR spectrum of trifluoromethoxybenzene (C6H5OCF3)⋯methanol with our earlier reported spectrum of anisole (C6H5OCH3)⋯methanol.

A close competition between O-HO and O-Hπ hydrogen bonding: IR spectroscopy of anisole-methanol complex in helium nanodroplets.

Anisole is a multifunctional molecule that can form intermolecular complexes via its aromatic π-electron system as well as its methoxy group. We have studied the complexation of anisole with methanol. This serves as a prototype system to explore the competition between O-HO, O-Hπ, C-HO and C-Hπ hydrogen bonding. The anisolemethanol molecular complexes were formed in superfluid helium droplets and were detected using high-resolution laser-infrared spectroscopy, in the frequency range between 2630 and 2730 cm-1 covering the O-D stretches of methanol-d4 (CD3OD). Several bands assigned to (anisole)m(methanol)n complexes (where m = 1, and 2 and n = 1) were observed. The experimental results are complemented by the ab initio electronic structure calculations at the MP2/6-311++G(d,p) and B3LYP-D3/aug-cc-pVTZ levels of theory. Based on a comparison of the observed spectra with the ab initio theoretical spectra, we suggest that for the anisolemethanol complex, structures bound via O-HO and O-Hπ hydrogen bonding are almost equally preferred.

Observation of the Low-Frequency Spectrum of the Water Trimer as a Sensitive Test of the Water-Trimer Potential and the Dipole-Moment Surface.

Intermolecular interactions in bulk water are dominated by pairwise and non-pairwise cooperative interactions. While accurate descriptions of the pairwise interactions are available and can be tested by precise low-frequency spectra of the water dimer up to 550 cm-1 , the same does not hold for the three-body interactions. Here, we report the first comprehensive spectrum of the water trimer in the frequency region from 70 to 620 cm-1 using helium-nanodroplet isolation and free-electron lasers. By comparison to accompanying high-level quantum calculations, the experimentally observed intermolecular bands can be assigned. The transition frequencies of the degenerate translation, the degenerate in-plane and the non-degenerate out-of-plane libration, as well as additional bands of the out-of-plane librational mode are reported for the first time. These provide a benchmark for state-of-the-art water potentials and dipole-moment surfaces, especially with respect to three-body interactions.

Isolation of a Halogen-Bonded Complex Formed between Methane and Chlorine Monofluoride and Characterisation by Rotational Spectroscopy and Ab Initio Calculations.

A halogen-bonded complex formed between methane and chlorine monofluoride has been isolated in the gas phase before the reaction between the components and has been characterised through its rotational spectrum, which is of the symmetric-top type but only exhibits K = 0 type transitions at the low effective temperature of the pulsed-jet experiment. Spectroscopic constants for two low-lying states that result from internal rotation of the CH4 subunit were detected for each of the two isotopic varieties H4C···35ClF and H4C···37ClF and were analysed to show that ClF lies on the symmetry axis with Cl located closer than F to the C atom, at the distance r0(C···Cl) ≅ 3.28 Å and with an intermolecular stretching force constant kσ ≅ 4 N m-1. Ab initio calculations at the explicitly correlated level CCSD(T)(F12c)/cc-pVTZ-F12 show that in the equilibrium geometry, the ClF molecule lies along a C3 axis of CH4 and Cl is involved in a halogen bond. The Cl atom points at the nucleophilic region identified on the C3 axis, opposite the unique C-H bond and somewhere near the C atom and the tetrahedron face centre, with re(C···Cl) = 3.191 Å. Atoms-in-molecules (AIM) theory shows a bond critical point between Cl and C, confirming the presence of a halogen bond. The energy that is required to dissociate the complex from the equilibrium conformation into its CH4 and ClF components is only De ≅ 5 kJ mol-1. A likely path for the internal rotation of the CH4 subunit is identified by calculations at the same level of theory, which also provide the variation of the energy of the system as a function of the motion along that path. The barrier to the motion along the path is only ≅ 20 cm-1.

Observation of the Low-Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces.

Using the helium nanodroplet isolation setup at the ultrabright free-electron laser source FELIX in Nijmegen (BoHeNDI@FELIX), the intermolecular modes of water dimer in the frequency region from 70 to 550 cm-1 were recorded. Observed bands were assigned to donor torsion, acceptor wag, acceptor twist, intermolecular stretch, donor torsion overtone, and in-plane and out-of-plane librational modes. This experimental data set provides a sensitive test for state-of-the-art water potentials and dipole moment surfaces. Theoretical calculations of the IR spectrum are presented using high-level quantum and approximate quasiclassical molecular dynamics approaches. These calculations use the full-dimensional ab initio WHHB potential and dipole moment surfaces. Based on the experimental data, a considerable increase of the acceptor switch and a bifurcation tunneling splitting in the librational mode is deduced, which is a consequence of the effective decrease in the tunneling barrier.

Acid solvation versus dissociation at "stardust conditions": Reaction sequence matters.

Chemical reactions at ultralow temperatures are of fundamental importance to primordial molecular evolution as it occurs on icy mantles of dust nanoparticles or on ultracold water clusters in dense interstellar clouds. As we show, studying reactions in a stepwise manner in ultracold helium nanodroplets by mass-selective infrared (IR) spectroscopy provides an avenue to mimic these "stardust conditions" in the laboratory. In our joint experimental/theoretical study, in which we successively add H2O molecules to HCl, we disclose a unique IR fingerprint at 1337 cm-1 that heralds hydronium (H3O+) formation and, thus, acid dissociation generating solvated protons. In stark contrast, no reaction is observed when reversing the sequence by allowing HCl to interact with preformed small embryonic ice-like clusters. Our ab initio simulations demonstrate that not only reaction stoichiometry but also the reaction sequence needs to be explicitly considered to rationalize ultracold chemistry.

Accessing different binding sites of a multifunctional molecule: IR spectroscopy of propargyl alcoholwater complexes in helium droplets.

We report high-resolution infrared spectroscopic studies on complexes of propargyl alcohol with water (D2O) molecules, formed in superfluid helium droplets. The spectra were recorded in the frequency ranges of 2605-2700 cm-1 and 2730-2820 cm-1, covering the symmetric and antisymmetric stretching vibrations of the bound D2O. Mass-selective infrared spectroscopic measurements, a variation of the band intensities with dopant partial pressures (pickup curves) and ab initio calculations, performed at the MP2/6-311++G(d,p) level of theory, reveal the formation of two local minimum structures for the 1 : 1 PAD2O cluster. These structures are bound via O-HO (with water as the H-bond donor) and -C[triple bond, length as m-dash]C-HO (with propargyl alcohol as the H-bond donor) interactions and are less stable by 4.9 kJ mol-1 and 12.7 kJ mol-1, respectively, as compared to the global minimum structure for the complex.

Helium droplet infrared spectroscopy of glycine and glycine-water aggregates.

Infrared absorption spectra of glycine and glycine-water aggregates embedded in superfluid helium nanodroplets were recorded in the frequency range 1000-1450 cm-1. For glycine monomer, absorption bands were observed at 1106 cm-1, 1134 cm-1, and 1389 cm-1. These bands were assigned to the C-OH stretch mode of the glycine conformers I, III and II, respectively. For glycine-water aggregates, we observed two bands at 1209 cm-1 and 1410 cm-1 which we assign to distinct conformers of glycine-H2O. In all cases, the water is found to preferentially bind to the carboxyl group of the glycine.

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond.

In this discussion, we show that a static definition of a 'bond' is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate 'hydrogen bonding' from 'van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg∙∙∙HX complexes (Rg=He/Ne/Ar and X=F/Cl/Br) and ethane-1,2-diol. Results for the Rg∙∙∙HX/DX complexes show that Rg∙∙∙DX could have a 'deuterium bond' even when Rg∙∙∙HX is not 'hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an 'intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the OO stretching, though a 'bond' is not found in the equilibrium structure. This dynamical 'bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration 'breaks' an existing bond and in the later case, a vibration leads to 'bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this 'hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition.

Rotational spectra of propargyl alcohol dimer: a dimer bound with three different types of hydrogen bonds.

Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer [A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and "Atoms in Molecules" analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O-H⋯O, O-H⋯π, and C-H⋯π. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact.

The X-C···π (X = F, Cl, Br, CN) carbon bond.

High-level ab initio calculations have been used to study the interactions between the CH3 group of CH3X (X = F, Cl, Br, CN) molecules and π-electrons. These interactions are important because of the abundance of both the CH3 groups and π-electrons in biological systems. Complexes between C2H4/C2H2 and CH3X molecules have been used as model systems. Various theoretical methods such as atoms in molecules theory, reduced density gradient analysis, and natural bond orbital analysis have been used to discern these interactions. These analyses show that the interaction of the π-electrons with the CH3X molecules leads to the formation of X-C···π carbon bonds. Similar complexes with other tetrel molecules, SiH3X and GeH3X, have also been considered.

Fe as hydrogen/halogen bond acceptor in square pyramidal Fe(CO)5.

Hydrogen bonded complexes formed between the square pyramidal Fe(CO)5 with HX (X = F, Cl, Br), showing X-H···Fe interactions, have been investigated theoretically using density functional theory (DFT) including dispersion correction. Geometry, interaction energy, and large red shift of about 400 cm(-1) in the HX stretching frequency confirm X-H···Fe hydrogen bond formation. In the (CO)5Fe···HBr complex, following the significant red-shift, the HBr stretching mode is coupled with the carbonyl stretching modes. This clearly affects the correlation between frequency shift and binding energy, which is a hallmark of hydrogen bonds. Atoms in Molecule (AIM) theoretical analyses show the presence of a bond critical point between the iron and the hydrogen of HX and significant mutual penetration. These X-H···Fe hydrogen bonds follow most but not all of the eight criteria proposed by Koch and Popelier (J. Phys. Chem. 1995, 99, 9747) based on their investigations on C-H···O hydrogen bonds. Natural bond orbital (NBO) analysis indicates charge transfer from the organometallic system to the hydrogen bond donor. However, there is no correlation between the extent of charge transfer and interaction energy, contrary to what is proposed in the recent IUPAC recommendation (Pure Appl. Chem. 2011, 83, 1637). The "hydrogen bond radius" for iron has been determined to be 1.60 ± 0.02 Å, and not surprisingly it is between the covalent (1.27 Å) and van der Waals (2.0) radii of Fe. DFT and AIM theoretical studies reveal that Fe in square pyramidal Fe(CO)5 can also form halogen bond with ClF and ClH as "halogen bond donor". Both these complexes show mutual penetration as well, though the Fe---Cl distance is closer to the sum of van der Waals radii of Fe and Cl in (CO)5Fe···ClH, and it is about 1 Å less in (CO)5Fe···ClF.

The X-C···Y (X = O/F, Y = O/S/F/Cl/Br/N/P) 'carbon bond' and hydrophobic interactions.

While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as -F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C···Y interaction, which could be called 'carbon bonding'. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the 'hydrophobic interactions'.

Microwave spectroscopic and atoms in molecules theoretical investigations on the Ar···propargyl alcohol complex: Ar···H-O, Ar···π, and Ar···C interactions.

The structure of the Ar···propargyl alcohol (Ar···PA) complex is determined from the rotational spectra of the parent complex and its two deuterated isotopologues, namely Ar···PA-D(OD) and Ar···PA-D(CD). The spectra confirm a geometry in which PA exists in the gauche form with Ar located in between -OH and -C≡C-H groups. All a, b and c types of transitions show small splitting due to some large-amplitude motion dominated by C-OH torsion, as in the monomer. Splittings in a- and b-type transitions are of the order of a few kilohertz, whereas splitting in the c-type transitions is relatively larger (0.9-2.6 MHz) and decreases in the order Ar···PA>Ar···PA-D(CD)>Ar···PA-D(OD). The assignments are well supported by ab initio calculations. Atoms in molecules (AIM) and electrostatic potential calculations are used to explore the nature of the interactions in this complex. AIM calculations not only reveal the expected O-H···Ar and π···Ar interactions in the Ar···gauche-PA complex, but also novel C···Ar (of CH2OH group) and O-H···Ar interactions in the Ar···trans-PA complex. Similar interactions are also present in the Ar···methanol complex.