State Rotational Transitions Research Articles

Transition State Stabilizing Effects of Oxygen and Sulfur Chalcogen Bond Interactions.

Non-covalent chalcogen bond (ChB) interactions have found utility in many fields, including catalysis, organic semiconductors, and crystal engineering. In this study, the transition stabilizing effects of ChB interactions of oxygen and sulfur were experimentally measured using a series of molecular rotors. The rotors were designed to form ChB interactions in their bond rotation transition states. This enabled the kinetic influences to be assessed by monitoring changes in the rotational barriers. Despite forming weaker ChB interactions, the smaller chalcogens were able to stabilize transition states and had measurable kinetic effects on the rotational barriers. Sulfur stabilized the bond rotation transition state by as much as -7.2 kcal/mol without electron-withdrawing groups. The key was to design a system where the sulfur -hole was aligned with the lone pairs of the chalcogen bond acceptor. Oxygen rotors also could form transition state stabilizing ChB interactions but required electron-withdrawing groups. For both oxygen and sulfur ChB interactions, a strong correlation was observed between transition state stabilizing abilities and electrostatic potential (ESP) of the chalcogen, providing a useful predictive parameter for the rational design of future ChB systems.

Stereoelectronic interactions are too weak to explain the molecular conformation in solid state of cis-2-tert-butyl-5-(tert-butylsulfonyl)-1,3-dioxane.

cis-2-tert-Butyl-5-(tert-butylsulfonyl)-1,3-dioxane (cis-1) exhibits a high degree of eclipsing in the H-C5-S-C segment in the solid state, the origin of which remains unexplained. The eclipsed conformation that corresponds to an energetic minimum in the solid state practically corresponds to a rotational transition state in solution, which allows an approach to understand transitions states. The difference in the enthalpy of sublimation ΔsubH between cis-1 and the more stable trans-1 is 8.40 kcal mol-1, lets to consider that the intermolecular interactions in the crystalline structure must be responsible for the conformational effect observed in the solid state. The study of the experimental electron density of cis-1 in solid state allowed to establish that CH⋯OS intermolecular interaction is the main contribution to the observed eclipsing. The charge density analysis was also performed using the quantum theory of atoms in molecules to evaluate the nature and relevance of the intermolecular interactions in the crystal structure.

Influence of Internal Noncovalent Bonds on Rotational Dynamics.

While a good deal of information has accumulated concerning the manner in which an intramolecular noncovalent bond can affect the relative energies of various conformers, less is known about how such bonds might affect the dynamics of interconversion between them. A series of molecules are constructed in which symmetrically equivalent conformers containing a noncovalent bond can be interconverted by a bond rotation, the energy barrier to which is computed by quantum chemical methods. The rotation of a CF3 group attached to a phenyl ring is speeded up if a Se··F chalcogen bond can be formed with a SeH or SeF group placed in an ortho position, a bond that is present in and stabilizes the rotational transition state. The analogous SnF3 group can, on the other hand, engage in a Sn··Se tetrel bond in its global minimum. The energetic cost of breakage of this bond is not fully compensated by the appearance of a Se··F chalcogen bond in the rotational transition state. Other systems were designed by placing two phenyl rings on opposite ends of an octahedrally disposed SeF4 group. A high barrier inhibits their rotation with bulky Br atoms in ortho positions, but this barrier is lowered if Br is replaced by groups that can engage in either chalcogen (SeH or SeF) or pnicogen (AsH2) bonds with the F atoms in the rotational transition state. The barrier reduction is closely related to the strength of these noncovalent bonds.

Pnictogen Interactions with Nitrogen Acceptors

AbstractStabilizing nitrogen pnictogen bond interactions were measured using molecular rotors. Intramolecular C=O⋅⋅⋅N interactions were formed in the bond rotation transition states which lowered the rotational barriers and increased the rates of rotation, as measured by EXSY NMR. The pnictogen interaction energies show a very strong correlation with the positive electrostatic potential on nitrogen, which was consistent with a strong electrostatic component. In contrast, the NBO perturbation and pyramidalization analyses show no correlation, suggesting that the orbital‐orbital component is minor. The strongest C=O⋅⋅⋅N pnictogen interactions were comparable to C=O⋅⋅⋅C=O interactions and were stronger than C=O⋅⋅⋅Ph interactions, when measured using the same N‐phenylimide rotor system. The ability of the nitrogen pnictogen interactions to stabilize transition states and enhance kinetic processes demonstrates their potential in catalysis and reaction design.

Rotation-Inversion Isomerization of Tertiary Carbamates: Potential Energy Surface Analysis of Multi-Paths Isomerization Using Boltzmann Statistics.

Potential energy surface (PES) analyses at the SMD[MP2/6-311++G(d,p)] level and higher-level energies up to MP4(fc,SDTQ) are reported for the fluorinated tertiary carbamate N-ethyl-N-(2,2,2-trifluoroethyl) methyl carbamate (VII) and its parent system N,N-dimethyl methyl carbamate (VI). Emphasis is placed on the analysis of the rotational barrier about the CN carbamate bond and its interplay with the hybridization of the N-lone pair (NLP). All rotational transition state (TS) structures were found by computation of 1D relaxed rotational profiles but only 2D PES scans revealed the rotation-inversion paths in a compelling fashion. We found four unique chiral minima of VII, one pair each of E- and Z-rotamers, and we determined the eight unique rotational TS structures associated with every possible E/Z-isomerization path. It is a significant finding that all TS structures feature N-pyramidalization whereas the minima essentially contain sp2 -hybridized nitrogen. We will show that the TS stabilities are affected by the synergetic interplay between NLP/CO2 repulsion minimization, NLP→σ* (CO) negative hyperconjugation, and two modes of intramolecular through-space electrostatic stabilization. We demonstrate how Boltzmann statistics must be applied to determine the predicted experimental rotational barrier based on the energetics of all eight rotamerization pathways. The computed barrier for VII is in complete agreement with the experimentally measured barrier of the very similar fluorinated carbamate N-Boc-N-(2,2,2-trifluoroethyl)-4-aminobutan-1-ol II. NMR properties of VII were calculated with a variety of density functional/basis set combinations and Boltzmann averaging over the E- and Z-rotamers at our best theoretical level results in good agreement with experimental chemical shifts δ(13 C) and J(13 C,19 F) coupling constants of II (within 6 %).

Nitrogen fractionation towards a pre-stellar core traces isotope-selective photodissociation

Context. Isotopologue abundance ratios are important to understand the evolution of astrophysical objects and ultimately the origins of a planetary system such as our own. With nitrogen being a fundamental ingredient of pre-biotic material, understanding its chemistry and inheritance is of fundamental importance to understand the formation of the building blocks of life. Aims. We aim to study the 14N/15N ratio in HCN, HNC, and CN across the prototypical pre-stellar core L1544. This study allows us to test the proposed fractionation mechanisms for nitrogen. Methods. We present here single-dish observations of the ground state rotational transitions of the 13C and 15N isotopologues of HCN, HNC, and CN with the IRAM 30 m telescope. We analyse their column densities and compute the 14N/15N ratio map across the core for HCN. The 15N fractionation of CN and HNC is computed towards different offsets across L1544. Results. The 15N-fractionation map of HCN towards a pre-stellar core is presented here for the first time. Our map shows a very clear decrease in the 14N/15N ratio towards the southern edge of L1544, where carbon chain molecules present a peak, strongly suggesting that isotope-selective photodissociation has a strong effect on the fractionation of nitrogen across pre-stellar cores. The 14N/15N ratio in CN measured towards four positions across the core also shows a decrease towards the south-east of the core, while HNC shows the opposite behaviour. We also measured the 12CN/13CN ratio towards four positions across the core. Conclusions. The uneven illumination of the pre-stellar core L1544 provides clear evidence that 15N fractionation of HCN and CN is enhanced towards the region more exposed to the interstellar radiation field. Isotope-selective photodissociation of N2 is then a crucial process to understand 15N fractionation, as already found in protoplanetary disks. Therefore, the 15N fractionation in pre-stellar material is expected to change depending on the environment within which pre-stellar cores are embedded. The 12CN/13CN ratio also varies across the core, but its variation does not affect our conclusions as to the effect of the environment on the fractionation of nitrogen. Nevertheless, the interplay between the carbon and nitrogen fractionation across the core warrants follow-up studies.

MULTICHARME: a modified Chernin-type multi-pass cell designed for IR and THz long-path absorption measurements in the CHARME atmospheric simulation chamber

Abstract. We have developed MULTICHARME, a modified Chernin-type multi-pass cell especially designed for IR and THz long-path absorption measurements in the CHamber for Atmospheric Reactivity and Metrology of the Environment (CHARME). By measuring the output power using a near-IR diode-laser and a THz amplified multiplication chain, we have established that the effective reflectivity of MULTICHARME is better than 94 % over approximately three decades of frequency. Absorption measurements of N2O have been performed by probing highly excited rovibrational transitions in the near-IR and ground state rotational transitions at submillimeter wavelengths. In each case the linearity of the absorbance with the path lengths was verified. Finally, we demonstrate that THz spectroscopy is able to study the isotopic composition of greenhouse polar gases such as N2O and to absolutely quantify stable (N2O) and reactive (O3) species at trace levels. At low pressure the ozone concentration was continuously monitored and its decay characterized. The deduced ozone lifetime of 3.4 ± 0.1 h is shorter compared with previous measurements performed in CHARME at atmospheric pressure. For the first time, the ability of THz rotational spectroscopy to monitor, with a very high degree of selectivity, stable and reactive polar compounds at trace level in an atmospheric simulation chamber is demonstrated. However, the sensitivity of the THz monitoring needs to be improved to reach atmospheric trace levels. For this purpose, it is necessary to fully understand the origin of the observed baseline variations caused by the complex multiple standing waves present in MULTICHARME.

Electrostatically-gated molecular rotors.

The ability to control molecular-scale motion using electrostatic interactions was demonstrated using an N-phenylsuccinimide molecular rotor with an electrostatic pyridyl-gate. Protonation of the pyridal-gate forms stabilizing electrostatic interactions in the transition state of the bond rotation process that lowers the rotational barrier and increases the rate of rotation by two orders of magnitude. Molecular modeling and energy decomposition analysis confirm the dominant role of attractive electrostatic interactions in lowering the bond rotation transition state.

Theoretical study on pentiptycene molecular brake: photoinduced isomerization and photoinduced electron transfer.

The isomerization of the double bond plays an important role in the braking and de-braking of the light-controlled molecular brake. Therefore, the pentiptycene-type (Pp-type) light-controlled molecular brake system ((E)- and (Z)-4'-pentiptycyl vinyl-[1,1'-biphenyl]-4-carbonitrile) containing the C = C double bond was theoretically studied. Combining the 6-31G(d) basis set, the ωB97XD functional with dispersion correction was applied to implement the (E)-configuration and (Z)-configuration initial optimization. Next, using the 6-311G(d,p) basis set, the relaxed potential energy surface scans of the rotation angle were operated, and then the optimization calculations of the transition states at the extremum high points. Analyzing the stagnation points and the rotational transition states on the potential energy profiles, the rotation mechanism and basic energy parameters of the molecular brake were obtained. Then, the DFT computations at ground states and the TD-DFT computations of vertical excitation energy were put into practice at the accuracy of the def-TZVP basis set for the two configurations, and using the natural transition orbital (NTO) analyses combining the excitation energies and absorption spectra, the electronic transition characteristics and electron transfer properties of light-controlled molecular brake were studied. Afterwards, in order to investigate the photoinduced isomerization reaction, the C = C double bond was scanned on the relaxed potential energy surface, and the intermediates of the isomerization reaction were searched and analyzed; thus, the braking mechanism of the light-controlled molecular brake was proposed.

Encapsulating N-Heterocyclic Carbene Binuclear Transition-Metal Complexes as a New Platform for Molecular Rotation in Crystalline Solid-State.

In crystalline solids, molecules generally have limited mobility due to their densely packed environment. However, structural information at the molecular level may be used to design amphidynamic crystals with rotating elements linked to rigid, lattice-forming parts, which may lead to molecular rotary motions and changes in conformation that determine the physical properties of the solid-state materials. Here, we report a novel design of emissive crystalline molecular rotors with a central pyrazine rotator connected by implanted transition metals (Cu or Au) to a readily accessible enclosure formed by two N-heterocyclic carbenes (NHC) in discrete binuclear complexes. The activation energies for the rotation could be tuned by changing the implanted metal. Exchanging Cu to Au resulted in an ∼4.0 kcal/mol reduction in the rotational energy barrier as a result of lower steric demand by elongation of the axle with the noble metal, and a stronger electronic stabilization in the rotational transition state by enhancement of the d-π* interactions between the metal centers and the pyrazine rotator. The Cu(I) rotor complex showed a greater electronic delocalization than the Au(I) rotor complex, causing a red-shifted solid-state emission. Molecular rotation-induced emission quenching was observed in both crystals. The enclosing NHC rotors are easy to prepare, and their rotational motion should be less dependent on packing structures, which are often crucial for many previously documented amphidynamic molecular crystals. The platform from the encapsulating NHC cationic metal complexes and the metal-centered rotation-axis provide a promising scaffold for a novel design of crystalline molecular rotors, including manipulation of rotary dynamics and solid-state emission.

Dual Local Oscillator SIS Receiver for Simultaneous Observations of Water Isotopologues in the Solar System

NASA's Planetary Decadal Survey Vision and Voyages has concluded that measurements of isotopic cometary water vapor, and in particular the deuterium-to-hydrogen ratio (D/H) ratio, are an important tool for unraveling the mysteries involving the origin of Earth's water, and the evolution of our solar system. To support this goal, we have developed, through an internal Jet Propulsion Laboratory research program, quantum-limited superconductor insulator superconductor (SIS) receivers covering the important 500 $-$ 600 GHz submillimeter frequency band. These instruments can detect the (1 $_{10}$ -1 $_{01}$ ) HDO rotational transition, and the (1 $_{10}$ -1 $_{01}$ ) ground state (rotational) transitions of Ortho H $_2^{16}$ O, H $_2^{17}$ O, and H $_2^{18}$ O with exquisite sensitivity. However, given the extremely weak HDO emission and the time-variability of the outgassing processes in comets, expeditious low noise D/H ratio measurements of these sources remain extremely challenging. To address this issue, we investigate the possibility of acquiring HDO, H $_2^{17}$ O, and H $_2^{18}$ O simultaneously by means of a novel dual local oscillator (2LO) down-conversion process, as an alternative to ultra—broadband IF bandwidth systems.

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines.

Fluorine-containing analogues of proline are valuable tools in engineering and NMR spectroscopic studies of peptides and proteins. Their use relies on the fundamental understanding of the interplay between the substituents and the main chain groups of the amino acid residue. This study aims to showcase the polarity-related effects that arise from the interaction between the functional groups in molecular models. Properties such as conformation, acid–base transition, and amide-bond isomerism were examined for diastereomeric 4-fluoroprolines, 4-(trifluoromethyl)prolines, and 1,1-difluoro-5-azaspiro[2.4]heptane-6-carboxylates. The preferred conformation on the proline ring originated from a preferential axial positioning for a single fluorine atom, and an equatorial positioning for a trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pKa values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors C4-exo conformation of the pyrrolidine ring.

A laboratory rotational study of the interstellar propynal

The discovery of propynal HCCCHO in the interstellar medium (ISM), has been reported in previous investigations, but its detection relied on only a few measured rotational transitions. Therefore, we provide in this work an exhaustive experimental study of its rotational spectra in the microwave, millimeter-wave (mm-wave), and sub-millimeter wave (sub-mm) regions from 6 to 480 GHz. We employed different but complementary spectroscopic techniques in the time and frequency domains. Chirped pulse Fourier transform microwave spectroscopy (CP-FTMW) from 6 to 18 GHz was used to measure and analyze the ground state rotational transitions of the three 13C isotopic species in their natural abundances. The Stark-modulation microwave spectroscopy allowed the identification of rotational spectra in excited vibrational states. The room temperature mm-wave and sub-mm wave spectroscopy made possible the study of the rotational spectra from 82 to 480 GHz in the ground state as well as in the five low-lying excited vibrational states. We have collected more than 2500 newly assigned transitions of propynal and determined very accurate sets of spectroscopic rotational constants for each state. Moreover, we have assigned about 200 rotational lines for the three 13C isotopologues. Reliable line-lists of frequencies are provided for further observations of this molecule in different interstellar regions.

Hindered rotational barriers in conjugated donor-acceptor substituted systems: calculations vs. experiments.

Quantum mechanical calculations of barriers to rotation within push-pull π-conjugated molecules involving strong electron donors (D) and acceptors (A) using the generally accepted approach fail to reproduce the experimental barriers determined by temperature-dependent NMR spectra. On the examples of seven derivatives of this type with substituents of varying electron donating and accepting strength, we find that determination of one of the rotational barriers, for instance, that of the acceptor substituent, requires not only the energy calculation of the respective transition state of this substituent, but also the transition state of the donor and the transition state involving both donor and acceptor substituents. Calculations of the rotation barriers using B3LYP and APFD functionals considering three transition states produce the results with mean absolute deviations from 10 experimental barriers of 0.28-0.19 kcal mol-1 depending on the basis set.

Relationship between Rotational Barriers and Charge Shifts.

Conjugation and hyperconjugation are closely related stereoelectronic effects that are usually discussed in a qualitative fashion. It is possible to make it more quantitative. The natural bond orbital method provides a means of estimating the energetic consequence. They may also be studied by a charge shift analysis. Rotational barriers are often appropriately discussed in terms of such effects where the rotational transition state has broken the interaction between donor and acceptor atoms or groups. A comparison of charge distribution between the ground state and the transition state will show how much charge transfer occurs and if any other atoms are involved. This has been studied for substituted vinyl methyl ethers, substituted N,N-dimethylvinylamines, p-substituted anilines, and some esters and amides. Linear relationships were found for the rotational barriers vs the charge shifts. For some compounds, the σ- and π-components of the charge were obtained and showed that competition for σ-charge can lead to changes in the π-charge. Cases where there cannot be charge transfer are also discussed.

Torsional splitting and the four-fold barrier to internal rotation: The rotational spectra of vinylsulfur pentafluoride.

Vinylsulfur pentafluoride (VSPF), a molecule with a four-fold internal rotor, -SF4, has been studied with high resolution Fourier transform microwave spectroscopy. We believe that this is the first report of resolved four-fold internal rotation. As such, we have presented the tools needed to understand and analyze such a problem. These include debugging the ERHAM computer program necessary to fit the spectra and the free rotor to high barrier correlation diagram necessary to understand the torsional states of the four-fold rotor. The A, E, and B torsional state rotational transitions are well resolved and assigned. Spectroscopic transitions of four isotopologues of VSPF, H2C=CH-SF5, the normal isotopologue, and the singly substituted 34S and 13C isotopologues were measured and assigned. Contrary to expectation, the A torsional state could not be fit with only a semi-rigid Hamiltonian. The barrier to internal rotation, V 4, is found to be 227 cm-1. Ab initio calculations at the MP2 aug-cc-pVQZ level of theory and basis set were performed and the results of this calculation are compared to our experimental results.

Influence of Rotator Design on the Speed of Self-Assembled Four-Component Nanorotors: Coordinative Versus Dispersive Interactions.

Four-component nanorotors are prepared by the self-assembly of stator [Cu4(4)]4+ with its four copper(I)-loaded phenanthroline stations and various rotators carrying one, two, or three pyridine terminals. The fourth component, 1,4-diazabicyclo[2.2.2]octane, serves as a connecting axle between rotator and stator. Capitalizing on the heteroleptic pyridyl and phenanthroline metal complexes concept, the rotator's pyridine terminals are connected to the copper(I)-loaded phenanthroline stations (Npy → [Cu(phen)]+) in the STOP state and disconnected in the transition state of rotation. As the barrier of the thermally activated rotation, measured by variable-temperature 1H NMR, is mainly governed by attractive forces between stator stations and rotator terminals, it increases along the series Ea (monopyridine rotator) < Ea (dipyridine rotator) < Ea (tripyridine rotator). However, there are even distinct differences in rate between rotors with equal number of rotator terminals. The change from the 5,10-dipyridyl (cis) to 5,15-dipyridyl (trans) zinc porphyrin rotator enhances the rotational frequency by almost 1000-fold. Density functional theory computational results suggest that not only coordinative Npy → [Cu(phen)]+ interactions but also dispersive attraction influence the barrier of rotation.

Ordered yttrium concentration effects on barium zirconate structure, proton binding sites and transition states

Acceptor doped perovskites show promise as fuel cell proton conducting ceramic membranes and continue to be rapidly developed. Proton conduction in barium zirconate with 6.25% ordered yttrium doping at the zirconium site is explored. The dopant increases octahedral distortions in the lattice similar to our earlier studied 12.5% dopant system though the angle distribution is slightly broader. Normal modes promoting vibrations about a non-transient octahedral tilt are found for both concentrations at frequencies thermally accessible at typical proton conduction temperatures. The energy of proton binding sites and transition states roughly increases with distance away from the dopant though there are many oscillations in the trend due to local proton induced distortions. Protons can both locally enhance and decrease the octahedral distortions induced by the dopant. Transition state energies roughly increase with proton-dopant distance. Rotational and intraoctahedral transfer transition state energies vary through a similar magnitude range though the intraoctahedral transition states are often higher in energy. Interoctahedral transfer transition states tend to have the highest energies. The diversity of minima and transition states suggests that proton conduction in 6.25% yttrium doped barium zirconate is more complex than conduction in 12.5% doped barium zirconate.

Computational investigation of π-bond strengths in fluorinated ethylenes

The strengths of π-bonds in a series of fluorinated ethylenes have been computationally investigated, and the potential energy surfaces for thermal CC bond rotation in fluorinated ethylenes, as well as in ethylene, have been explored. The computed thermal rotational barrier values and the π-bond strengths obtained using Benson’s procedure show parallel trends. Our calculations indicate that the π-bond in CH2=CHF is slightly stronger, and the one in CF2=CF2 is noticeably weaker than that in CH2=CH2. In addition, the stabilization effects of fluorine substitution have been evaluated for fluorinated ethylene molecules and for singlet biradical thermal rotation transition states. Considering these fluorine substituent effects, the change in the π-bond strength of a series of fluorinated ethylenes can be qualitatively interpreted.

Conformational analysis, energy profile, and structural-electronic properties evaluation of mephedrone derivatives employing quantum-mechanical models

Mephedrone (4-methyl-meth-cathinone) or 4-MMC and its derivative 3-MMC are analogs of cathinone which act as non-selective substrates for monoamine transporters, facilitating a neurotransmitter release via the reversal of normal transporter fluxes. The pharmacological effects like paranoia, hallucinations, euphoria, aggressiveness, and psychosis make these molecules “abusive designer drugs.” In the present study, conformations of all isomers of 3- and 4-MMC have been studied at the quantum-chemical level. Calculations have been performed using Møller-Plesset second-order (MP2) methods with 6-31G(d, p) basis sets. Present study shows that there are low-energy conformers for the meta (3-MMC) and para (4-MMC) isomers that are connected by way of low-barrier transition states. Natural bond orbital (NBO) analyses have been also performed to corroborate the results as estimated from the MP2 calculations. The molecular electrostatic potential surface data for each molecule has been calculated, revealing likely that reaction sites and probable metabolism pathway for both derivatives have been proposed. IR spectra for MMC derivatives have been compared with experimental data, and rotational transition states connecting all conformers have been reported.