H-bonded clusters in the trimethylamine/water system: a matrix isolation and computational study

The environmentally important interaction products of trimethylamine (TMA) and water molecules have been observed by Matrix Isolation Fourier Transform Infrared Spectroscopy (MIS-FTIR). Infrared spectra of solid argon matrix layers, in which both TMA and H(2)O molecules were entrapped as impurities, were analyzed for bands in the ν(O-H) region, not seen in matrix layers containing either of the parent molecules alone. Results were interpreted on the basis of the emergence of several spectral band pairs and their red shifts from the position of the matrix isolated H(2)O monomers as compared to semiempirically scaled frequencies from the B3LYP/aug-cc-pVTZ calculations and empirical correlations with a large body of data on H-bonded complexes. Bands were assigned to a complex cluster of two TMA molecules flanking a closed ring of four H-bonded H(2)O molecules. The formation of this cluster is argued to be formed in the vapor phase (as opposed to being a result of diffusion of the trapped species) and is related to its large stabilization energy (enthalpy) because of strong cooperative effects in its H-bond system.     

Intermolecular vibrations of the water trimer, a matrix isolation study

Infrared spectra from 25 to 4000 cm(-1) have been recorded of water (H2O, D2O and H218O) matrix isolated in neon, argon, and krypton matrices. Intermolecular absorption bands of different isotopologues of the water trimer and tetramer have been assigned from concentration dependencies and diffusion behavior, using the well-known mid-infrared trimer and tetramer absorption bands as measures of the trimer and tetramer concentrations. The results are compared to ab initio calculations.     

Formamide dimers: a computational and matrix isolation study

The dimerization of formamide (FMA) has been investigated by matrix isolation spectroscopy, static ab initio calculations, and ab initio molecular dynamics (AIMD) simulations. Comparison of the experimental matrix IR spectra with the ab initio calculations reveals that two types of dimers A and C are predominantly formed, with two and one strong NH...O hydrogen bonds, respectively. This is in accordance with previously published experiments. In addition, there is also experimental evidence for the formation of the thermally labile dimer B after deposition of high concentrations of FMA in solid xenon. The AIMD simulations of the aggregation process show that in all cases dimer C is initially formed, but rearrangement to the more stable doubly hydrogen-bonded structures A or B occurs for a fraction of collisions on the sub-picosecond time scale.     

Complexes of atmospheric alpha-dicarbonyls with water: FTIR matrix isolation and theoretical study

The complexes of glyoxal (Gly), methylglyoxal (MGly), and diacetyl (DAc) with water have been studied using Fourier transform infrared (FTIR) matrix isolation spectroscopy and MP2 calculations with 6-311++G(2d,2p) basis set. The analysis of the experimental spectra of the Gly(MGly,DAc)/H2O/Ar matrixes indicates formation of one Gly...H2O complex, three MGly...H2O complexes, and two DAc...H2O ones. All the complexes are stabilized by the O-H...O(C) hydrogen bond between the water molecule and carbonyl oxygen as evidenced by the strong perturbation of the O-H, C=O stretching vibrations. The blue shift of the CH stretching vibration in the Gly...H2O complex and in two MGly...H2O ones suggests that these complexes are additionally stabilized by the improper C-H...O(H2) hydrogen bonding. The theoretical calculations confirm the experimental findings. They evidence the stability of three hydrogen-bonded Gly...H2O and DAc...H2O complexes and six MGly...H2O ones stabilized by the O-H...O(C) hydrogen bond. The calculated vibrational frequencies and geometrical parameters indicate that one DAc..H2O complexes, two Gly...H2O, and three MGly...H2O ones are additionally stabilized by the improper hydrogen bonding between the C-H group and water oxygen. The comparison of the theoretical frequencies with the experimental ones allowed us to attribute the calculated structures to the complexes present in the matrixes.     

Photolysis of water/dicyanoacetylene complexes: an infrared matrix isolation and theoretical study

The structure and energy of the 1:1 complexes formed between dicyanoacetylene and water (D₂O) in argon matrix are investigated using FTIR spectroscopy and ab initio calculations at the B3LYP/6-31g** level of theory. Two types of 1:1 complexes are observed. The first one corresponds to the NH structure characterized by a hydrogen bond between H₂O and one of the nitrogen of dicyanoacetylene. The second corresponds to the CO form which involves a van der Waals interaction between the Cβ of dicyanoacetylene and the oxygen of water.

These complexes were irradiated with an Hg–Xe lamp at 10 K. Two products were observed by FTIR spectroscopy. The first one corresponds to the Isonitrile:H₂O complexes formation. The second one, resulting from the reaction of water on the photolyzed dicyanoacetylene, corresponds to the cyanoketene:HCN complex formation.     

The role of relaxation in the nuclear spin conversion process

The nuclear spin conversion rate depends on the collisions, which break the coherence created by magnetic intramolecular interactions between pairs of quasi degenerate levels belonging to the different spin isomers. The collisions act similarly to break the coherence created by a radiation field between two levels inducing pressure broadening of molecular transitions. Collisional relaxation rates have been extensively studied in this last situation using semi-classical approach and rectilign trajectory for collisional path.Taking advantage of the analogy, the present paper shows that calculations can be efficiently adapted for the collisional relaxation terms present in the ‘quantum relaxation’ model of nuclear spin conversion.For ¹³CH₃F, numerous experimental measurements of spin conversion rates in the presence of an electric field have allowed to derive directly relaxation rates. Our calculation appears to agree satisfactorily with these experimental values. For ¹²CH₃F, calculated relaxations rates are also given for the pairs involved in nuclear spin conversion.     

Molecular-dynamics study of photodissociation of water in crystalline and amorphous ices

We present the results of classical dynamics calculations performed to study the photodissociation of water in crystalline and amorphous ice surfaces at a surface temperature of 10 K. A modified form of a recently developed potential model for the photodissociation of a water molecule in ice [S. Andersson et al., Chem. Phys. Lett. 408, 415 (2005)] is used. Dissociation in the top six monolayers is considered. Desorption of H(2)O has a low probability (less than 0.5% yield per absorbed photon) for both types of ice. The final outcome strongly depends on the original position of the photodissociated molecule. For molecules in the first bilayer of crystalline ice and the corresponding layers in amorphous ice, desorption of H atoms dominates. In the second bilayer H atom desorption, trapping of the H and OH fragments in the ice, and recombination of H and OH are of roughly equal importance. Deeper into the ice H atom desorption becomes less important and trapping and recombination dominate. Motion of the photofragments is somewhat more restricted in amorphous ice. The distribution of distances traveled by H atoms in the ice peaks at 6-7 Angstroms with a tail going to about 60 Angstroms for both types of ice. The mobility of OH radicals is low within the ice with most probable distances traveled of 2 and 1 Angstrom for crystalline and amorphous ices, respectively. OH is, however, quite mobile on top of the surface, where it has been found to travel more than 80 Angstroms. Simulated absorption spectra of crystalline ice, amorphous ice, and liquid water are found to be in very good agreement with the experiments. The outcomes of photodissociation in crystalline and amorphous ices are overall similar, but with some intriguing differences in detail. The probability of H atoms desorbing is 40% higher from amorphous than from crystalline ice and the kinetic-energy distribution of the H atoms is on average 30% hotter for amorphous ice. In contrast, the probability of desorption of OH radicals from crystalline ice is much higher than that from amorphous ice.     

Conformers and photochemistry of propyl nitrites: a matrix isolation study

The infrared spectra of both constitutional isomers (n and i) of propyl nitrite have been recorded in an Ar matrix. Conformational analysis and assignments of the vibrational transitions have been carried out on the basis of quantum chemical calculations. Assignment of spectral lines to different conformers was also aided experimentally, by utilizing the different rate of photodecomposition of the conformers, as well as by employing conformational cooling using a supersonic jet as the inlet source for matrix deposition. The rate of photodecomposition is primarily determined by the steric alignment of the nitrite group, whereas jet cooling affects mainly the conformation of the alkyl tail. On the basis of these experimental observations and computational predictions two to three conformers of isopropyl nitrite and eight conformers of n-propyl nitrite were identified. After broadband ultraviolet-visible (UV-vis) photolysis of isopropyl nitrite in the matrix, HNO, acetone, HNO.acetone complex, acetaldehyde, and nitrosomethane were identified as the main products. Furthermore, in a small amount, NO and possibly the isopropoxy radical were also present in the matrix. Photolysis of n-propyl nitrite yielded HNO, propanal, and their 1:1 complex as the main products together with a small amount of NO and cis-1-nitrosopropanol.     

Vibrational spectrum of m-benzyne: a matrix isolation and computational study

m-Benzyne (2) was generated in low-temperature matrices and IR spectroscopically characterized from four different precursors. To assign the IR absorptions, the perdeuterated derivative 2-d(4) was also investigated. By comparison with CCSD(T) calculations all vibrations between 200 and 2500 cm(-)(1) with a predicted relative intensity >2% could be assigned. All experimental and theoretical results are in accordance with a biradicaloid structure for 2, while there is no evidence for a bicyclic closed-shell structure. While benzyne 2 is stable under the conditions of matrix isolation at low temperature, flash vacuum pyrolysis at high temperatures or UV irradiation results in the rearrangement to cis-enediyne. A mechanism involving ring opening accompanied by hydrogen migration is proposed.     

Reactions of late lanthanide metal atoms with water molecules: a matrix isolation infrared spectroscopic and theoretical study

The reactions of late lanthanide metal atoms (Gd-Lu) with water molecules have been investigated using matrix isolation infrared spectroscopy. The reaction intermediates and products were identified on the basis of isotopic substitution experiments and density functional theory calculations. All of the metal atoms except Lu react with water to form the M(H2O) complexes spontaneously upon annealing (M = Gd, Tb, Dy, Ho, Er, Tm, and Yb). The Dy(H2O) and Ho(H2O) complexes are able to coordinate a second water molecule to form the Dy(H2O)2 and Ho(H2O)2 complexes. The M(H2O) complexes isomerize to the inserted HMOH isomers under visible light irradiation, which further decompose to give the MO and/or HMO molecules upon UV light irradiation. The M(OH)2 molecules (M = Gd-Lu) were also produced. The results have been compared with our earlier work covering the early lanthanide metal atoms (Nd, Sm, Eu) to observe the existent trends for the lanthanide metal atom reactions.     

Entangled electron and nuclear spin states in 15N@C60: density matrix tomography

Procedures of the preparation and detection of entangled electron-nuclear spin states in (15)N@C(60) by combining electron spin resonance and electron nuclear double resonance pulse techniques are presented. A quantitative evaluation of the complete density matrix is obtained by a special density matrix tomography. All four Bell states of a two qubit subsystem were analyzed and experimental decoherence times are presented. In addition, we estimate a quantum critical temperature of T(q)=7.76 K for this system at an electron spin resonance frequency of 95 GHz.     

Structural properties and thermodynamics of water clusters: a Wang-Landau study

The temperature dependence of structural properties and thermodynamic behavior of water clusters has been studied using Wang-Landau sampling. Four potential models, simple point charge/extended (SPC/E), transferable intermolecular potential 3 point (TIP3P), transferable intermolecular potential 4 point (TIP4P), and Gaussian charge polarizable (GCP), are compared for ground states and properties at finite temperatures. Although the hydrogen bond energy and the distance of the nearest-neighbor oxygen pair are significantly different for TIP4P and GCP models, they approach to similar ground state structures and melting transition temperatures in cluster sizes we considered. Comparing with TIP3P, SPC/E model provides properties closer to that of TIP4P and GCP.     

N-Hydroxyurea dimers: A matrix isolation and theoretical study

The dimerization of N-hydroxyurea (NH₂CONHOH) has been investigated by FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-311++G(2d,2p) calculations. The analysis of NH₂CONHOH/Ar matrix spectra and comparison with theoretical ones reveal the formation of two types of dimers with a strong OH⋯O hydrogen bond. There is an additional weak interaction between the oxygen atom of the OH group of the proton donor molecule and the NH or NH₂ group of the proton acceptor in both dimers, respectively. The identified structures correspond to local minima on the PES. The formation of the less stable structures not the most stable ones indicates that the creation of N-hydroxyurea dimers is related to the dipole-dipole interaction at the initial stage of the dimerization process, which favours generation of polar dimers.     

Isomerical and structural determination of N-hydroxyurea: a matrix isolation and theoretical study

The structure, isomerization pathways and vibrational spectra of the important N-hydroxyurea (HU) molecule were studied by matrix isolation FT-IR spectroscopy and molecular orbital calculations undertaken at the MP2/6-311++G(2d,2p) level of theory. In agreement with theoretical predictions, 1Ea represents the most stable keto isomer in the gas-phase, being the dominant species trapped in argon matrices, while the 1Za isomer also contributes to the spectrum of isolated HU molecules. According to the calculated abundance values at the temperature of evaporation of the compound (393 K), the 1Ea and 1Za isomers together with a small contribution of 1Eb are expected to appear in the experimental spectra. Since the barrier for interconversion 1Ea? 1Eb is only ～2 kJ mol(-1), these two isomers are in equilibrium in the matrices and, at low temperature, the population of the less stable 1Eb form is too small to be observed. Full assignment of the observed spectra of N-hydroxyurea and its deuterium analogue was undertaken on the basis of comparison with theoretical data.     

Conformations of trimethyl phosphite: a matrix isolation infrared and ab initio study

The conformations of trimethyl phosphite (TMPhite) were studied using matrix isolation infrared spectroscopy. TMPhite was trapped in a nitrogen matrix using an effusive source maintained at two different temperatures (298 and 410 K) and a supersonic jet source. The experimental studies were supported by ab initio computations performed at the B3LYP/6-31++G** level. Computations identified four minima for TMPhite, corresponding to conformers with C(1)(TG(±)G(±)), C(s)(TG(+)G(-)), C(1)(G(±)TT), and C(3)(G(±)G(±)G(±)) structures, given in order of increasing energy. Computations of the transition state structures connecting the C(s)(TG(+)G(-)) and C(1)(G(±)TT) conformers to the global minimum C(1)(TG(±)G(±)) structure were also carried out. The barriers for the interconversion of C(s)(TG(+)G(-)) and C(1)(G(±)TT) to the ground state C(1)(TG(±)G(±)) conformer were 0.2 and 0.6 kcal/mol, respectively. Comparison of conformational preferences of TMPhite with the related carbon compound, trimethoxymethane, and the organic phosphate, trimethyl phosphate, was also made using natural bond orbital analysis.     

Nitroxide paramagnet-induced para-ortho conversion and nuclear spin relaxation of H2 in organic solvents

The kinetics of para-ortho conversion and nuclear spin relaxation of H 2 in chloroform- d 1 were investigated in the presence of nitroxides as paramagnetic catalysts. The back conversion from para-hydrogen ( p-H 2) to ortho-hydrogen ( o-H 2) was followed by NMR by recording the increase in the intensity of the signal of o-H 2 at regular intervals of time. The nitroxides proved to be hundreds of times more effective at inducing relaxation among the spin levels of o-H 2 than they are in bringing about transitions between p-H 2 and the levels of o-H 2. The value of the encounter distance d between H 2 and the paramagnetic molecule, calculated from the experimental bimolecular conversion rate constant k 0, using the Wigner theory of para-ortho conversion, agrees perfectly with that calculated from the experimental relaxivity R 1 using the force free diffusion theory of spin-lattice relaxation.     

The conversion among various B4C clusters: a density functional theoretical study

Geometry optimizations and vibration frequencies of B4C clusters were performed with Becke-3LYP method using 6-31G(d) basis set. We have found 14 stable isomers, and the most stable structure among them is the five-member ring containing two three-member boron rings. We also analyzed these stable isomers in detail, and the results show that the structures containing three-member boron rings are predominant in energy for B4C clusters. In terms of MO and NBO analysis, the three-centered bond and the pi-electron delocalization play an important role in stabilizing the planar five-member rings of these B4C clusters. Our calculations suggest that isomer4 can be converted into isomer7 with only an energy barrier of 0.31 kJ mol(-1) at the B3LYP/6-311G+(3df) level. Although the planar structures of the five-member rings (isomers12-14) can be converted with each other, the conversions of isomer14 to isomer13 and isomer13 to isomer12 have high-energy barriers of 70.99 and 68.51 kJ mol(-1) at the B3LYP/6-31G(d) level, respectively.     

Cyanoacetylene adsorption on amorphous and crystalline water ice films: investigation through matrix isolation and quantum study.

The structure and energy properties of the 1:1 complexes formed between cyanoacetylene and H2O (D2O) are investigated using FT-IR matrix isolation spectroscopy and ab initio calculations at the MP2/ 6-31G(d,p) level. Cyanoacetylene adsorption and desorption on amorphous ice film are monitored by FT-IR using the temperature-programmed desorption method. In an argon matrix, two types of 1:1 complexes are observed. The first one corresponds to the NH structure, which involves a hydrogen bond with the terminal nitrogen of cyanoacetylene. The second corresponds to the HO form, which involves a hydrogen bond from the cyanoacetylene to the oxygen of water. This last complex is the more stable (DeltaE = -8.1 kJ/mol.). As obtained in argon matrixes, two kinds of adsorption site are observed between HC3N and ice. The first one, stable between 25 and 45 K is characterized by a nu(OH) shift similar to the one observed in matrix for the NH complex. The second, stable at higher temperatures (between 45 and 110 K), corresponds to an interaction with the dangling oxygen site of ice and is similar to the HO complex observed in matrix. From theoretical calculations (DFT method combined with a plane wave basis set and ultrasoft pseudopotentials), it is shown that, for this adsorption site, the HC3N moiety is flattened on the ice surface and stabilized by a long-distance interaction ( approximately 3 A) between one dangling OH and the pi system of the C triple bond C triple bond. The HC3N desorption occurs between 110 and 140 K, and the associated desorption energy is 39 kJ/mol. This value is in good agreement with the first principle calculation based on density functional theory and ultrasoft pseudopotentials (34 kJ/mol). These calculations confirm the electrostatic nature of the interaction forces. A small amount of cyanoacetylene is incorporated into the bulk and desorbs at the onset of the ice crystallization near 145 K. In these two kinds of experiments, HC3N acts as both an electrophilic and a nucleophilic molecule.     

A theoretical investigation of the relative stability of hydrated glycine and methylcarbamic acid--from water clusters to interstellar ices

We have theoretically investigated how the low-energy conformers of the neutral and the zwitterionic forms of glycine as well as methylcarbamic acid are stabilized by the presence water. The MP2/6-311++G(d,p) method was utilized to conduct calculations on glycine and methylcarbamic acid in both isolated clusters and in clusters embedded in the conductor-like polarizable continuum model (C-PCM), where the clusters explicitly contain between one and ten water molecules. The neutral forms of glycine and methylcarbamic acid were found to have similar hydration energies, whereas the neutral methylcarbamic acid was determined to be approximately 32 kJ mol(-1) more stable than the neutral glycine in the isolated clusters and 30 kJ mol(-1) more stable in the C-PCM embedded clusters. Both the number and strength of the hydrogen bonding interactions between water and the zwitterions drive the stability. This lowers the relative energy of the glycine zwitterion from 50 kJ mol(-1) above neutral glycine, when there are two water molecules in the clusters to 11 kJ mol(-1) below for the clusters containing ten water molecules. For the methylcarbamic acid clusters with two water molecules, the zwitterion is 51 kJ mol(-1) higher in energy than the neutral form, but it remains 13 kJ mol(-1) above the neutral methylcarbamic acid in the clusters containing ten water molecules. When the bulk water environment is simulated by the C-PCM calculations, we find both the methylcarbamic acid and glycine zwitterionic forms have similar energies at 20 kJ mol(-1) above the neutral methylcarbamic acid energy and 10 kJ mol(-1) lower than the neutral glycine energy. Although neither methylcarbamic acid nor glycine have been detected in the interstellar medium yet, our findings indicate that methylcarbamic acid is the more stable product from methylamine and carbon dioxide reactions in a water ice. This suggests that methylcarbamic acid likely plays a role in the intermediate steps if glycine is formed in the interstellar medium.