Higher Energy Isomer Research Articles

From the trimer, through the pentamer, to liquid water

High resolution spectra, obtained for small water clusters in the Vibrational-Rotational-Tunneling spectroscopy experiments in Saykally's group, provide invaluable data that should guide us in untangling the quite elusive properties of liquid water [PNAS 98 (2001) 10533]. Recently, we suggested that the bifurcation splittings in cyclic water trimers originate from the tunneling of hydrogen bonded protons in a mean field, double well potential between two oxygen neighbors [Chem.Phys.Lett. 661 (2016) 263]. Based on the similar/corresponding pattern of splittings in cyclic water pentamers, the model developed for the trimer should be also applicable to pentamers. Assuming that pentamers are major transient components in the fluctuating hydrogen bonded network of water, the model is applied to liquid water. In this paper, we show that our 1-D model gives surprisingly good agreement with experimental 2-D spectra in the OH stretch region of liquid water, reported by Tokmakoff's group [JCP 145 (2016) 094501]. Our results strengthen the hypothesis that cyclic pentamers should be considered as transiently present in the liquid, and that their fused structures form low density liquid. We also postulate that the higher energy isomers of the pentamer contribute to high density liquid water.

Ab initio investigation of possible lower-energy candidate structure for cationic water cluster (H2O) 12+ via particle swarm optimization method

Detecting the underlying performance of hydrated electrons and hydroxyl radicals in the cationic water cluster can greatly help to understand the inter reaction mechanism in the liquid water and aqueous solutions. Based on our previous (H2O)10+ research, we have paid attention to more problems of larger cationic clusters in this work, including the existence of hemibonded type, long-range correction functions, and hydrogen-bonded site analyses. The lower-energy structures of the cationic water cluster (H2O)12+ have been comprehensively explored, and more experienced functions are introduced to check the ground state and vibration spectrum. Unlike the configuration regularity of neutral (H2O)12 clusters and small cationic water clusters, those new-found structures for (H2O)12+ are inclined to adopt three dimension (3D) cage-like structures and the H2O-OH2 structure appears in the higher energy isomer. The calculation reveals that the lowest stable isomer is the 3D cage structure W14 predicted at MP2 level, which has not been reported yet. In the thermal simulation, structure transition from the cage-like to the ring-like occurs at T > ≈256 K, and the two dimension (2D) ring-like structure occupies a dominant position at high temperature range. The infrared spectra explain that the difference of the spectra between the 2D net structures and 3D cage-structures is mainly caused by the weight fluctuation of single acceptor-single donor (AD), double acceptor-single donor (AAD), and single acceptor-double donor (ADD) sites in these isomers. This further gives a similarity relation between (H2O)12+ and H+(H2O)12 clusters in the shape of the network and spectral characteristics. By molecular orbitals and topological analysis, we find that the lone pair orbital on hydroxyl radical dominates the reactivity and stability of cationic system. The present research may be helpful for exploring the evolution law of the larger cationic water clusters in the future.

Vibrational properties of small rhodium clusters: role of magnetism, charge state, and isomerization effects

Extensive density functional theory calculations dedicated to analyze the structure, electronic properties, and vibrational behavior of small and positively charged rhodium clusters are presented. Following the experimental results of Harding et al. [D.J. Harding et al., J. Chem. Phys. 133, 214304-1 (2010)] Rh19+ , Rh11+ , Rh12+ , and Rh13+ clusters are considered and the infrared (IR) spectra for various structural isomers is simulated. The calculations reveal a complex interplay between the distribution and intensity of the IR active frequencies with the atomic structure, magnetism, and charge state of the systems, as well as the crucial role played by high-energy isomers to explain experimental data. Based on a direct comparison between theory and experiment we predict that, for Rh9+, a weighted average of simulated IR spectra corresponding to our lowest energy 9-atom cubic cluster and the closest in energy compact isomer can yield an acceptable agreement between theory and experiment. The possibility of considering mixtures of various IR spectra to explain the measured data is supported by nudged-elastic-band calculations that reveal the existence of inter-conversion processes between different isomers with relatively small energy barriers ( ~0.6 eV). In addition, the recent observation of bi-exponential decays in reactivity experiments of rhodium clusters interacting with N2O species around those sizes also supports this claim. For Rh11+ and Rh12+ clusters, we also obtain that compact high-energy structures with low spin magnetizations are the ones having an IR spectra more in agreement with experiments. Finally for the most common compact and cubic Rh13+ clusters considered in the literature, for which there are no experimental IR spectra to compare with, well defined vibrational features are predicted which could help to identify the atomic configuration of this highly relevant structure.

Infrared Photodissociation Spectra of [Sn(CO2) n]- Cluster Ions.

We present infrared spectra and density functional theory calculations of mass selected [Sn(CO2) n]- cluster anions ( n = 2-6). The spectra and structures of these clusters exhibit less structural diversity than those of analogous clusters with first-row transition metals, but are more complex than those for the heavy coinage metals or for the related [Bi(CO2) n]- clusters. The most favorable core ion structure for all cluster sizes can be characterized as a Sn-oxalate complex, Sn[C2O4]-. Higher energy isomers based on a bidentate η2-(C,O) CO2 ligand tightly bound to the metal atom in SnCO2- complexes are also observed, even for the largest cluster sizes studied here. For n = 2, another high energy isomer is found, featuring a CO2 ligand weakly bound to the metal atom in a SnCO2- ion.

A Possible Progenitor of the Interstellar Sulfide Bond: Rovibrational Characterization of the Hydrogen Disulfide Cation HSSH+

Abstract S2H (HSS) has been observed very recently in the interstellar medium, specifically in the Horsehead nebula. The protonated form, S2H2 +, is believed to be a necessary intermediate in its creation in the gas phase in UV-irradiated regions. However, little is known about this radical cation. This work showcases that the trans-HSSH+ isomer is 0.12 eV lower in energy than the cis with a 1.05 eV upper limit to the torsional rotation barrier. Additionally, the vibrational frequencies and rotational constants for both structures are provided in full here for the first time. The cis isomer is likely the more detectable since it possesses a permanent dipole moment and has a high-intensity vibrational frequency for the antisymmetric H−S−S bend at 926 cm−1 (10.8 μm), in the heart of the mid-IR spectral range. A third isomer, H2S−S+ is also reported herein lying ∼0.9 eV in energy above trans-HSSH+. This isomer could play a role in the formation of S2H since it would be kinetically favored in the reaction of sulfur cations with hydrogen sulfide. Further assessment of this third, higher-energy isomer is left for future work.

Stable NCNgNSi (Ng=Kr, Xe, Rn) Compounds with Covalently Bound C-Ng-N Unit: Possible Isomerization of NCNSi through the Release of the Noble Gas Atom.

Although the noble gas (Ng) compounds with either Ng-C or Ng-N bonds have been reported in the literature, compounds containing both bonds are not known. The first set of systems having a C-Ng-N bonding unit is predicted herein through the analysis of stability and bonding in the NCNgNSi (Ng=Kr-Rn) family. While the Xe and Rn inserted analogues are thermochemically stable with respect to all dissociation channels, but for the one producing CNSiN and free Ng, NCKrNSi has another additional three-body dissociation channel, NCKrNSi→CN+Kr+NSi, which is exergonic by -9.8 kcal mol-1 at 298 K. This latter dissociation can be hindered by lowering the temperature. Moreover, the NCNgNSi→Ng+CNSiN dissociation is also kinetically prohibited by a quite high free energy barrier ranging from 25.2 to 39.3 kcal mol-1 , with a gradual increase in going from Kr to Rn. Therefore, these compounds are appropriate candidates for experimental realization. A detailed bonding analysis by employing natural bond orbital, electron density, energy decomposition, and adaptive natural density partitioning analyses indicates that both Ng-N and C-Ng bonds in the title compounds are covalent in nature. In fact, the latter analysis indicates the presence of delocalized 3c-3e σ-bond within the C-Ng-N moiety and a totally delocalized 5c-2e σ-bond in these compounds. This is an unprecedented bonding characteristic in the sense that the bonding pattern in Ng inserted compounds is generally represented as the presence of covalent bond in one side of Ng, and the ionic interaction in the other side. Further, the dissociation of Ng from NCNgNSi facilitates the formation of a higher energy isomer of NCNSi, CNSiN, which cannot be formed from bare NCNSi as such, because of the very high free energy barrier associated with the isomeric transformation. Therefore, in the presence of Ng atoms it might be possible to detect the high energy isomer.

Structural properties of small Lin (n = 5–8) atomic clusters via ab initio random structure searching: A look into the role of different implementations of long-range dispersion corrections

In this work, we looked into the lowest energy structures of small lithium clusters (Lin, n = 5, 6, 7, 8) utilizing conventional PBE exchange–correlation functional, PBE with D2 dispersion correction and PBE with Tkatchenko and Scheffler (TS) dispersion correction, and searched using ab initio random structure searching. Results show that in general, dispersion-corrected PBE obtained similar lowest minima structures as those obtained via conventional PBE regardless of the type of implementation, although both D2 and TS found several high-energy isomers that conventional PBE did not arrive at, with TS in general giving more structures per energy range that could be attributed to its environment-dependent implementation. Moreover, D2 and TS dispersion corrections found a lowest energy geometry for Li8 cluster that is in agreement with the structure obtained via the typical benchmarking method diffusion Monte Carlo in a recent work. It is thus suggested that for much larger lithium clusters, utilization of dispersion correction could be of help in searching for lowest energy minima that is in close agreement with that of diffusion Monte Carlo results, but computationally inexpensive.

Ab initio molecular dynamics studies of formic acid dimer colliding with liquid water.

Ab initio molecular dynamics simulations of formic acid (FA) dimer colliding with liquid water at 300 K have been performed using density functional theory. The two energetically lowest FA dimer isomers were collided with a water slab at thermal and high kinetic energies up to 68kBT. Our simulations agree with recent experimental observations of nearly a complete uptake of gas-phase FA dimer: the calculated average kinetic energy of the dimers immediately after collision is 5 ± 4% of the incoming kinetic energy, which compares well with the experimental value of 10%. Simulations support the experimental observation of no delayed desorption of FA dimers following initial adsorption. Our analysis shows that the FA dimer forms hydrogen bonds with surface water molecules, where the hydrogen bond order depends on the dimer structure, such that the most stable isomer possesses fewer FA-water hydrogen bonds than the higher energy isomer. Nevertheless, even the most stable isomer can attach to the surface through one hydrogen bond despite its reduced hydrophilicity. Our simulations further show that the probability of FA dimer dissociation is increased by high collision energies, the dimer undergoes isomerization from the higher energy to the lowest energy isomer, and concerted double-proton transfer occurs between the FA monomers. Interestingly, proton transfer appears to be driven by the release of energy arising from such isomerization, which stimulates those internal vibrational degrees of freedom that overcome the barrier of a proton transfer.

Nitrile versus isonitrile adsorption at interstellar grain surfaces

Context. Almost 20% of the ~200 different species detected in the interstellar and circumstellar media present a carbon atom linked to nitrogen by a triple bond. Of these 37 molecules, 30 are nitrile R-CN compounds, the remaining 7 belonging to the isonitrile R-NC family. How these species behave in their interactions with the grain surfaces is still an open question. Aims. In a previous work, we have investigated whether the difference between nitrile and isonitrile functional groups may induce differences in the adsorption energies of the related isomers at the surfaces of interstellar grains of various nature and morphologies. This study is a follow up of this work, where we focus on the adsorption on carbonaceous aromatic surfaces. Methods. The question is addressed by means of a concerted experimental and theoretical approach of the adsorption energies of CH3CN and CH3NC on the surface of graphite (with and without surface defects). The experimental determination of the molecule and surface interaction energies is carried out using temperature-programmed desorption in an ultra-high vacuum between 70 and 160 K. Theoretically, the question is addressed using first-principle periodic density functional theory to represent the organised solid support. Results. The adsorption energy of each compound is found to be very sensitive to the structural defects of the aromatic carbonaceous surface: these defects, expected to be present in a large numbers and great diversity on a realistic surface, significantly increase the average adsorption energies to more than 50% as compared to adsorption on perfect graphene planes. The most stable isomer (CH3CN) interacts more efficiently with the carbonaceous solid support than the higher energy isomer (CH3NC), however.

Binuclear Cyclopentadienylmetal Methylene Sulfur Dioxide Complexes of Rhodium and Iridium Related to a Photochromic Metal Dithionite Complex.

The photochromic dithionite complex Cp*2Rh2(μ-CH2)2(μ-O2SSO2) (Cp* = η5-Me5C5) is of interest because it undergoes an unusual fully reversible unimolecular photochemical rearrangement to the isodithionite complex Cp*2Rh2(μ-CH2)2(μ-O2SOSO). In order to obtain more insight into these systems, a comprehensive density functional theory study has been carried out on isomeric Cp2M2(CH2)2(SO2)2 (M = Rh, Ir) derivatives. The experimentally observed rhodium complexes with coupled sulfur dioxide (SO2) units to give dithionite or isodithionite ligands are surprisingly high-energy kinetic isomers in our analysis, reflecting the need for dithionite rather than SO2 for their synthesis. Many isomeric structures containing two separate SO2 ligands are found to lie at lower energies than these dithionite and isodithionite complexes. In the lowest-energy Cp2M2(CH2)2(SO2)2 isomers, the two methylene groups couple to form an ethylene ligand that can be either terminal or bridging. In slightly higher energy structures, a formal hydrogen shift is predicted to occur within the ethylene ligand to give a methylcarbene CH3CH ligand. Isomers with a bridging methylcarbene ligand are energetically preferred over isomers with a terminal methylcarbene ligand. Generation of the lower-energy Cp2Rh2(CH2)2(SO2)2 isomers containing separate SO2 ligands should be achievable through reactions of SO2 with more highly reduced cyclopentadienylrhodium methylene complexes such as Cp*2Rh2(μ-CH2)2.

Silicon amino acids

AbstractThe existence and gas phase stability of silicon analogues of three natural amino acids (i.e., silicon glycine, silicon alanine, and silicon valine) belonging to the novel class of compounds termed silicon amino acids (SiAA) are investigated theoretically on the basis of ab initio QCISD/aug‐cc‐pVTZ and MP2/aug‐cc‐pVTZ calculations. All molecules studied (in their gas phase canonical forms) are structurally comparable to their proteinogenic counterparts (i.e., glycine, l‐alanine, and l‐valine) and capable of forming several structural isomers as such. These higher energy isomers are characterized by small relative energies (not exceeding 4 kcal mol−1). The simulated IR spectra of the Si‐Gly, Si‐Ala, and Si‐Val global minima are also presented and discussed.

The collision-free photochemistry of methyl azide at 157 nm: Mechanism and energy release.

Synchrotron radiation VUV-photoionization based photofragment translational spectroscopy was used to identify the primary and secondary photodissociation reactions of methyl azide (CH3N3) at 157 nm under collision-free conditions. Two primary dissociation channels are identified, leading to CH3 + N3 (the radical channel) and CH3N + N2 (the molecular elimination channel). The last channel is the major dissociation pathway, but unlike work at longer photolysis wavelengths, here, the radical channel exclusively produces the higher energy isomer cyclic-N3. Product time-of-flight data for both channels were obtained and compared with earlier work on methyl azide photochemistry at 193 nm based on electron impact ionization, allowing us to estimate a product branching ratio ΦCH3-N3 ΦCH3N-N2 =2.3%±0.6%97.7%±0.6%.

High-Level Quantum Calculations of the IR Spectra of the Eigen, Zundel, and Ring Isomers of H+(H2O)4 Find a Single Match to Experiment.

The protonated water tetramer H+(H2O)4, often written as the Eigen cluster, H3O+(H2O)3, plays a central role in studies of the hydrated proton. The cluster has been investigated spectroscopically both experimentally and theoretically with some differences and controversies. The major issue stems from the existence of higher-energy Zundel isomers of this cluster and the role these isomers might play in the IR spectra. Settling this fundamental issue is one goal of this Communication, where high-level quantum calculations of the IR spectra of the Eigen and three isomeric forms of this cluster are presented. These calculations make use of a many-body representation of the potential and dipole moment surfaces and VSCF/VCI calculations of vibrational eigenstates and the IR spectrum. The calculated spectra for the Eigen H3O+(H2O)3 and D3O+(D2O)3 isomers compare very well with experiment. The calculated spectra for the cis and trans-Zundel and ring isomers show prominent features that do not match with experiment but which can guide future experiments to search for these interesting and important isomers.

A DFT Study on the Stabilization of the B≡B Triple Bond in a Metallaborocycle: Contrasting Electronic Structures of Boron and Carbon Analogues.

The electronic structure of (η5 -Cp)2 Zr(NH2 -BB-NH2 ) (3 b) suggests that it could be a candidate for having a boron-boron triple bond in the cyclic system; however, computational studies shows that 3 b is a very high energy isomer on its potential energy surface. Replacement of amines with tricoordinate nucleophilic boron groups (η5 -Cp)2 Zr[B(PH3 )2 -BB-B(PH3 )2 ] (3 c) reduces the relative energy dramatically. The B≡B triple bond arises through the donation of two electrons from the metal fragment, ZrCp2 , to the in-plane π-bonding orbital of the central B-B unit. Strong σ-donating and chelating bis-phosphine ligands (Me2 P(CH2 )n PMe2 ), which stabilize donor-acceptor bonding interaction in gem-diborene L2 B-BBr2 (10), would be a good choice along the synthetic path towards 3 d, (η5 -Cp)2 Zr[B4 (Me2 P(CH2 )3 PMe2 )2 ]. A comparison of the energetics of the reaction leading to a cyclic boryne system (3 d), with the linear boryne isomer [(B2 NHCPh )2 ] shows that the angle strain from cyclization is compensated by stabilization from the metal.

Initiation Reactions in Acetylene Pyrolysis.

In gas-phase combustion systems the interest in acetylene stems largely from its role in molecular weight growth processes. The consensus is that above 1500 K acetylene pyrolysis starts mainly with the homolytic fission of the C-H bond creating an ethynyl radical and an H atom. However, below ∼1500 K this reaction is too slow to initiate the chain reaction. It has been hypothesized that instead of dissociation, self-reaction initiates this process. Nevertheless, rigorous theoretical or direct experimental evidence is lacking, to an extent that even the molecular mechanism is debated in the literature. In this work we use rigorous ab initio transition-state theory master equation methods to calculate pressure- and temperature-dependent rate coefficients for the association of two acetylene molecules and related reactions. We establish the role of vinylidene, the high-energy isomer of acetylene in this process, compare our results with available experimental data, and assess the competition between the first-order and second-order initiation steps. We also show the effect of the rapid isomerization among the participating wells and highlight the need for time-scale analysis when phenomenological rate coefficients are compared to observed time scales in certain experiments.

Nitrile versus isonitrile adsorption at interstellar grains surfaces

Context. Almost 20% of the ~200 different species detected in the interstellar and circumstellar media present a carbon atom linked to nitrogen by a triple bond. Among these 37 molecules, 30 are nitrile R-CN compounds, the remaining seven belonging to the isonitrile R-NC family. How these species behave in presence of the grain surfaces is still an open question. Aims. In this contribution we investigate whether the difference between nitrile and isonitrile functional groups may induce differences in the adsorption energies of the related isomers at the surfaces of interstellar grains of different nature and morphologies. Methods. The question was addressed by means of a concerted experimental and theoretical study of the adsorption energies of CH3CN and CH3NC on the surface water ice and silica. The experimental determination of the molecule – surface interaction energies was carried out using temperature programmed desorption (TPD) under an ultra-high vacuum (UHV) between 70 and 160 K. Theoretically, the question was addressed using first principle periodic density functional theory (DFT) to represent the organized solid support. Results. The most stable isomer (CH3CN) interacts more efficiently with the solid support than the higher energy isomer (CH3NC) for water ice and silica. Comparing with the HCN and HNC pair of isomers, the simulations show an opposite behaviour, in which isonitrile HNC are more strongly adsorbed than nitrile HCN provided that hydrogen bonds are compatible with the nature of the model surface. Conclusions. The present study confirms that the strength of the molecule surface interaction between isomers is not related to their intrinsic stability but instead to their respective ability to generate different types of hydrogen bonds. Coupling TPD to first principle simulations is a powerful method for investigating the possible role of interstellar surfaces in the release of organic species from grains, depending on the environment.

Molybdenum chloride catalysts for Z-selective olefin metathesis reactions.

The development of catalyst-controlled stereoselective olefin metathesis processes has been a pivotal recent advance in chemistry. The incorporation of appropriate ligands within complexes based on molybdenum, tungsten and ruthenium has led to reactivity and selectivity levels that were previously inaccessible. Here we show that molybdenum monoaryloxide chloride complexes furnish higher-energy (Z) isomers of trifluoromethyl-substituted alkenes through cross-metathesis reactions with the commercially available, inexpensive and typically inert Z-1,1,1,4,4,4-hexafluoro-2-butene. Furthermore, otherwise inefficient and non-stereoselective transformations with Z-1,2-dichloroethene and 1,2-dibromoethene can be effected with substantially improved efficiency and Z selectivity. The use of such molybdenum monoaryloxide chloride complexes enables the synthesis of representative biologically active molecules and trifluoromethyl analogues of medicinally relevant compounds. The origins of the activity and selectivity levels observed, which contradict previously proposed principles, are elucidated with the aid of density functional theory calculations.

Detection of a higher energy isomer of the CO-N2O van der Waals complex and determination of two of its intermolecular frequencies.

Infrared spectra in the carbon monoxide CO stretch region (∼2150 cm-1) and in the ν3 asymmetric stretch region of N2O (∼2223 cm-1) are assigned to the previously unobserved O-bonded form of the CO-N2O dimer ("isomer 2"). This van der Waals complex has a planar skewed T-shaped structure like that of the previously observed C-bonded form ("isomer 1"), but with the CO rotated by 180°. The effective intermolecular distance between the centers of mass is 3.51 Å for isomer 2 as compared to 3.88 Å for isomer 1. In addition to the fundamental band, two combination bands are observed for isomer 2, yielding values for two intermolecular vibrational modes: 14.502(5) cm-1 for the coupled disrotatory motion or the uncoupled CO rock and 21.219(5) cm-1 for the out-of-plane rock. We show that the published ab initio study on this system is inadequate in predicting the intermolecular frequencies for isomer 2 of CO-N2O.

Aromaticity-Controlled Energy Storage Capacity of the Dihydroazulene-Vinylheptafulvene Photochromic System.

Photochemical conversion of molecules into high-energy isomers that, after a stimulus, return to the original isomer presents a closed-cycle of light-harvesting, energy storage, and release. One challenge is to achieve a sufficiently high energy storage capacity. Here, we present efforts to tune the dihydroazulene/vinylheptafulvene (DHA/VHF) couple through loss/gain of aromaticity. Two derivatives were prepared, one with aromatic stabilization of DHA and the second of VHF. The consequences for the switching properties were elucidated. For the first type, sigmatropic rearrangements of DHA occurred upon irradiation. Formation of a VHF complex could be induced by a Lewis acid, but addition of H2 O resulted in immediate regeneration of DHA. For the second type, the VHF was too stable to convert into DHA. Calculations support the results and provide new targets. We predict that by removing one of the two CN groups at C-1 of the aromatic DHA, the heat storage capacity will be further increased, as will the life-time of the VHF. Calculations also reveal that a CN group at the fulvene ring retards the back-reaction, and we show synthetically that it can be introduced regioselectively.

Energetic Properties and Electronic Structure of [Si,N,S] and [Si,P,S] Isomers.

Correlated molecular orbital theory at the coupled cluster CCSD(T) level with augmented correlation consistent basis sets has been used to predict the structure and energetic properties of the isomers of [Si,N,S] and [Si,P,S]. The predicted ground states are linear (2)SNSi and cyclic (2)SPSi. The other two isomers are predicted to be ∼20 to 50 kcal/mol less stable than the ground state. The excess spin is mainly on S for (2)SNSi and on P for (2)SPSi. The calculated total atomization energies with the CBS limits derived from different methods differ by ∼2 kcal/mol. The results provide the best available heats of formation for these species. The bond dissociation energies (BDEs) in (2)SNSi are comparable to those in the corresponding diatomic molecules. For cyclic (2)SPSi, the formation of (4)P + (2)SSi requires less energy than the other bond dissociation processes. The BDEs in the higher energy isomers are substantially smaller than the corresponding diatomic species.