Fluxional Research Articles

Torsional control of the methyl group in methanol

Experimental and theoretical investigations of the field-free alignment of the nonrigid methanol molecule are reported. The molecule is subject to a $140\ensuremath{-}\mathrm{TW}/{\mathrm{cm}}^{2}$-intensity laser pulse with a 100-fs duration. The experimental signal displays a constant permanent alignment and a fast decaying transient alignment consistent with a prolatelike molecule with $(B+C)/2$ on the order of $0.808\phantom{\rule{0.28em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$. The theoretical model takes into account the large-amplitude internal rotation of the methyl group with respect to the hydroxyl group. In the case of a continuous-wave laser field, a rotational alignment close to that of a rigid molecule is predicted. Torsional alignment also occurs even though there is no explicit dependence of the polarizability tensor on the angle of internal rotation. In the case of a strong short laser pulse, the theoretical approach shows that permanent and transient rotational alignment take place. The latter displays an exponential-like decay due to the high density of rotation-torsion levels. Torsional alignment also occurs and depends on the temperature. The theoretical model allows us to reproduce the experimental signal provided one component of the polarizability tensor is adjusted and dissipation effects due to molecular collisions are taken into account.

A conceptual approach to the formation of paramagnetic nanospecies of noble metals

Abstract The general concepts are analyzed regarding the approach for the formation of paramagnetic species of noble metals, with a non-rigid (labile) molecule being used as a supporting matrix. The formation of the metal nanospecies follows three stages: (i) the metal ions are captured by the matrix, (ii) the reducing agent causes formation of individual atoms separated by the matrix fragments, (iii) the individual atoms agglomerate due to conformational transformations of the labile molecule-matrix. This algorithm is realized in two distinct systems: Ag-containing nanospecies embedded within the system of polyacrylic acid (PAA) chains grafted to the film of fluorinated ethylene propylene copolymer (FEP) and Au-containing nanospecies in the free matrix of tannin-citrate- oxo-hydroxo aluminate. The evolution of the electron paramagnetic resonance (EPR) spectra while cooling down demonstrates the appearance of the exchange interaction which is suppressed at higher temperatures by the vibrational modes of the molecule-matrix. The role of the oxo-hydroxo aluminate form is one of a molecular motor sorting the individual nanospecies by their size and charge state.

Disentangling the IR spectra of 2,3,3,3-tetrafluoropropene using an ab initio description of vibrational polyads by means of canonical Van Vleck perturbation theory

The vibrational spectra of 2,3,3,3-tetrafluoropropene (2333TFP) are studied in the infrared experimentally and theoretically by the canonical second-order Van Vleck operator perturbation theory (CVPT2) and full quartic potential energy surface (PES). 2333TFP belongs to hydrofluoroolefins (HFOs) considered among the most promising alternatives to the hydrofluorocarbons presently in use in refrigeration. The medium resolution infrared spectra of gaseous 2333TFP were recorded in the range 9500–30 cm−1. The integrated IR intensities for all bands falling between 6300–400 cm−1 were accurately determined. Theoretical descriptions of up to four-quanta anharmonic vibrational states of 2333TFP are performed using the state-of-the-art numerical-analytic implementation of CVPT2. High quality harmonic frequencies, obtained at different coupled-cluster levels of theory up to the CCSD(T*)-F12c/VTZ-F12 model were combined with the full quartic MP2/cc-pVTZ anharmonic force field to form the hybrid PES. All Fermi and Darling-Dennison resonances were detected using a universal criterion and treated with the variational CVPT2/VCI stage by using two-, three-, and four-quanta harmonic oscillator basis sets. General recommendations for choosing such basis sets in future studies are formulated. In addition to all fundamentals and their resonance satellites, the vibrational analysis led to the assignment of virtually all observed first/second overtone and binary/ternary combination bands. Computed dipole moment first derivatives in the principal axis system yielded reliable predictions of band shapes for fundamental transitions in good agreement with observed counterparts. Computed anharmonic IR intensities showed an excellent agreement with observed data in the measured ranges. The fundamental spectroscopic effect of excited resonances is observed experimentally and explained theoretically as a universal mechanism of formation of vibrational polyads. The efficiency of the CVPT2/VCI approach employed is clearly demonstrated and can be considered as a benchmark for modeling vibrational states and interpretation of vibrational spectra of semi-rigid molecules.

Reduced rovibrational coupling Cartesian dynamics for semiclassical calculations: Application to the spectrum of the Zundel cation.

We study the vibrational spectrum of the protonated water dimer, by means of a divide-and-conquer semiclassical initial value representation of the quantum propagator, as a first step in the study of larger protonated water clusters. We use the potential energy surface from the work of Huang et al. [J. Chem. Phys. 122, 044308 (2005)]. To tackle such an anharmonic and floppy molecule, we employ fully Cartesian dynamics and carefully reduce the coupling to global rotations in the definition of normal modes. We apply the time-averaging filter and obtain clean power spectra relative to suitable reference states that highlight the spectral peaks corresponding to the fundamental excitations of the system. Our trajectory-based approach allows for the physical interpretation of the very challenging proton transfer modes. We find that it is important, for such a floppy molecule, to selectively avoid initially exciting lower energy modes, in order to obtain cleaner spectra. The estimated vibrational energies display a mean absolute error (MAE) of ∼29 cm-1 with respect to available multiconfiguration time-dependent Hartree calculations and MAE ∼ 14 cm-1 when compared to the optically active experimental excitations of the Ne-tagged Zundel cation. The reasonable scaling in the number of trajectories for Monte Carlo convergence is promising for applications to higher dimensional protonated cluster systems.

Effects of NaCl concentration on electrical resistivity of clay with cooling

The influence of salt concentration and gravimetric water content on the freezing process of clay soil is studied by using electrical resistivity as a measurement. Along with the ultrasonic pulse method, the P-wave velocity of samples is obtained to estimate the unfrozen water content of frozen soil, and the development of cracks due to frost heave at different temperatures is also analyzed. The results indicate that the freezing temperatures of samples with a sodium chloride (NaCl) concentration of 0, 2% and 5% are −4 °C, −6 °C and −5 °C respectively. Cracks due to frost heave propagate rapidly at temperatures below the crack coalescence temperature, which results in a steep increase in electrical resistivity. There is a sigmoid function for the relationship between electrical resistivity and temperature. A good power function is found for the relationship between electrical resistivity and the NaCl concentration of clay soil. There is a power function for the relationship between the electrical resistivity of pore water and salinity. The electrical resistivity decreases linearly with water content at temperatures above freezing but increases logarithmically at temperatures below freezing. The generalized relationships between electrical resistivity and water content, NaCl concentration and temperature are effective for predicting the electrical resistivity of frozen saline soil in practice.

Experimental and theoretical conformational studies of hydrazine derivatives bearing a chromene scaffold

A conformational study of two novel hydrazine derivatives bearing a chromene moiety was carried out using ab initio and DFT quantum chemical methods, dynamic NMR and IR spectroscopy. The theoretical calculations predict and the experimental NOESY spectra confirm the (E)-anti,anti conformation as the most stable one in solution for the compounds (N'-[(E)-(2-methyl-2H-1-benzopyran-3-yl)methylidene]benzohydrazide and 4-hydroxy-N'-[(E)-(2-methyl-2H-1-benzopyran-3-yl)methylidene]benzohydrazide). The barriers of rotation around the amide bond in the studied compounds, ΔG≠, are in the range of 14.8–15.9 kcal mol−1 and were reproduced very well by the DFT calculations at the SMD/B3LYP/6-31+G(d,p) level of theory. The GIAO 1H and 13C chemical shifts calculated in DMSO and chloroform are in very good agreement with the experimental NMR data.

Group-theoretical formulation of an Eckart-frame kinetic energy operator in curvilinear coordinates for polyatomic molecules.

A new procedure is presented for building a general kinetic energy operator expressed as a polynomial series expansion of symmetry-adapted curvilinear coordinates for semirigid polyatomic molecules. As a starting point, the normal-mode Watson kinetic energy part is considered and then transformed into its curvilinear counterpart. An Eckart molecular fixed-frame is thus implicitly used. To this end, we exploit symmetry at all stages of the calculation and show how group-theoretically based methods and Γ-covariant tensors help properly invert nonlinear polynomials for the coordinate changes. Such a linearization procedure could also be useful in different contexts. Unlike the usual normal mode approach, the potential part initially expressed in curvilinear coordinates is not transformed in this work, making convergence of the Hamiltonian expansion generally faster. For dimensionality reduction, the final curvilinear kinetic and potential parts are expanded in terms of irreducible tensor operators when doubly and triply degenerate vibrations are involved. The procedure proposed here is general and can be applied to arbitrary Abelian and non-Abelian point groups. Illustrative examples will be given for the H2S (C2v), H2CO (C2v), PH3 (C3v), and SiH4 (Td) molecules.

Structural and Conformational Studies on Carboxamides of 5,6-Diaminouracils—Precursors of Biologically Active Xanthine Derivatives

8-Arylethynylxanthine derivatives are potent, selective adenosine A2A receptor antagonists, which represent (potential) therapeutics for Parkinson’s disease, Alzheimer’s dementia, and the immunotherapy of cancer. 6-Amino-5-amidouracil derivatives are important precursors for the synthesis of such xanthines. We noticed an unexpected duplication of NMR signals in many of these uracil derivatives. Here, we present a detailed analytical study of structurally diverse 6-amino-5-carboxamidouracils employing dynamic and two-dimensional NMR spectroscopy, density functional theory calculations, and X-ray analysis to explain the unexpected properties of these valuable drug intermediates.

Vibrational analysis of the ubiquitous interstellar molecule cyclopropenylidene (c-C3H2): the importance of numerical stability

Recent work on cyclopropenylidene, c-CH, sought to improve on past ab initio results with a complete basis set (CBS) quartic force field method capable of predicting fundamental bands to within 5 cm−1 accuracy of gas-phase spectroscopy experiments for semirigid molecules. It was suggested that a problematic coupling between n-body correlation and 1-particle basis set effects prevented a proper application of this method for the out-of-plane bending vibrations of c-CH. We establish here that the actual source of this anomalous behaviour is numerical instability in the out-of-plane bending quartic force constants. It is found that the use of the normal equations to solve for the quartic force field, as well as a bending coordinate grid which is too compact, leads to errors of ca. 20 cm−1 in and . Our revised analysis shows and to be 980 cm−1 and 777 cm−1, respectively.

Photoregulated fluxional fluorophores for live-cell super-resolution microscopy with no apparent photobleaching

Photoswitchable molecules have multiple applications in the physical and life sciences because their properties can be modulated with light. Fluxional molecules, which undergo rapid degenerate rearrangements in the electronic ground state, also exhibit switching behavior. The stochastic nature of fluxional switching, however, has hampered its application in the development of functional molecules and materials. Here we combine photoswitching and fluxionality to develop a fluorophore that enables very long (>30 min) time-lapse single-molecule localization microscopy in living cells with minimal phototoxicity and no apparent photobleaching. These long time-lapse experiments allow us to track intracellular organelles with unprecedented spatiotemporal resolution, revealing new information of the three-dimensional compartmentalization of synaptic vesicle trafficking in live human neurons.

A synthesis of new 7-amino-substituted 4-aminopyrazolo[1,5-a][1,3,5]triazines via a selective three-component triazine ring annulation

3-Amino-substituted 5-aminopyrazoles were found to be suitable substrates for the synthesis of new 4-aminopyrazolo[1,5-a][1,3,5]triazines (5-aza-9-deaza-adenines) when used in the one-pot, three-component reaction with cyanamide and triethyl orthoformate under microwave irradiation. The reaction proceeded selectively and its scope was demonstrated by the preparation of a library of 4-aminopyrazolo[1,5-a][1,3,5]triazines. Some structural aspects of the prepared compounds were investigated using dynamic NMR spectroscopy and X-ray crystallography. The operational simplicity, short reaction time, and good reproducibility are attractive features of the developed robust and practical approach for the synthesis of 7-amino-substituted 4-aminopyrazolo[1,5-a][1,3,5]triazines.

Synthesis, characterization and conformational study of new α,β-unsaturated acylhydrazones based on calix [4]arene backbone

A series of six new p-tert-butylcalix [4]arene-1,3-N,N′-diacylhydrazone derivatives 1–6 have been synthesized starting from β-chloro-α,β-unsaturated aldehydes and p-tert-butylcalix [4]arene hydrazide. They were characterized by IR, (1H, 13C, 19F) NMR and HRMS. In addition of the E/Z isomers around the CC bond of the starting aldehydes, the NMR data showed three conformers due to NC(O) bond rotation: transamid/transamid; Cisamid/transamid and Cisamid/Cisamid resulting from the disubstitution of calix [4]arenes. The rotational barriers around NC(O) bond for most compounds were measured in dimethylsulfoxide using dynamic NMR spectroscopy (DNMR). The results are discussed and compared with those previously reported for related β-chloro-α,β-unsaturated acylhydrazones.

On the use of reduced-density matrices for the semi-automatic assignment of vibrational states

ABSTRACTThe use of one- and two-mode reduced-density matrices (RDM), and , respectively, and in particular the use of their diagonal elements, and , is suggested for the assignment of normal-mode-like quantum numbers to variationally computed vibrational wave functions of semirigid molecules when the computation is based on a nuclear-motion Hamiltonian expressed in curvilinear internal coordinates . The use of RDMs for the semi-automatic assignment of vibrational states is tested on the HO molecule, whereby about the first 250 states, in the energy range of 0–25,000 cm−1, are assigned. The proposed semi-automatic assignment procedure takes advantage of the fact that (a) for semirigid molecules it is often possible to define internal coordinates which mimick normal coordinates defined by the harmonic counterparts of the anharmonic vibrations, (b) overlaps between already assigned and yet unassigned RDMs provide outstanding and often unambiguous suggestions for the quantum numbers, and (c) an energy-decomposition scheme helps to decide among possible assignment possibilities suggested by the computed density overlaps.

Synthesis of Bullvalenes: Classical Approaches and Recent Developments

The goal of this short review is to provide an overview of the different synthetic methodologies applied along the years for the synthesis of bullvalenes, prototypical fluxional molecules that were key in the understanding of valence tautomerism phenomena. Some interesting applications of these unique shapeshifting compounds are also presented.1 Introduction2 Classical Syntheses of Bullvalenes3 Recent Developments in the Synthesis of Bullvalenes4 Applications of Bullvalenes5 Conclusion

Unraveling Confined Dynamics of Guests Trapped in Self-Assembled Pd6L4 Nanocages by Ultrafast Mid-IR Polarization-Dependent Spectroscopy.

Self-assembled coordination cages form host-guest complexes through weak noncovalent interactions. Knowledge of how these weak interactions affect the structure, reactivity, and dynamics of guest molecules is important to further the design principles of current systems and optimize their specific functions. We apply ultrafast mid-IR polarization-dependent pump-probe spectroscopy to probe the effects of two Pd6L4 self-assembled nanocages on the properties and dynamics of fluxional group-VIII metal carbonyl guest molecules. We find that the interactions between the Pd6L4 nanocages and guest molecules act to alter the ultrafast dynamics of the guests, restricting rotational diffusional motion and decreasing the vibrational lifetime.

How do halogen atoms influence the competition between all-trans and hairpin conformers of unbranched alkanes?

Influence of fluorine, chlorine, and bromine atoms on conformational preferences of free non-rigid molecules is analyzed on the basis of quantum chemical calculations. Thirty-six compounds are considered: 35 with the general formula X(CH2)nY (where X = Y = CH3, F, Cl, Br or X = F, Cl, Br, Y = CH3 and even n from 8 to 16) and n-octane. According to the previous computational and experimental results obtained by other researches, free n-alkane molecules with the number of carbon atoms (nC) greater than approximately 16–18 prefer to form hairpin conformers (where the chain is folded in two) instead of fully extended (all-trans) conformers that are more favorable for the compounds with lower nC. For halogenated n-alkanes, such investigation is made for the first time. Calculations at the ωB97X-D/6–31++G(d,p) level of theory were performed for all compounds and at the MP2/6–31++G(d,p) level for n-alkanes, 1,n-difluoro-, 1,n-dichloroalkanes with n from 8 to 16, 1,8-dibromooctane and 1,9-fluoro-, 1,9-chloro-, 1,9-bromononane. Conclusions about influence of X, Y, or n on conformational preferences drawn from the calculations on the different theoretical levels are in qualitative agreement. The most prominent distinctions are revealed for tetradecane and 1,14-dichlorotetradecane. It is found that differences in the electronic (ΔEel) and electronic plus zero-point (ΔE0) energies between the hairpin and all-trans conformers have similar tendencies by variations of X, Y, or n. When the ΔEel and ΔE0 values for the particular compound are close to zero and have opposite signs, the distance between X and Y equal to ~ 4.0 A or less is an indicator for the preference of the hairpin conformer. The most strong effect on the advantageousness of the hairpin conformers is caused by two bromine atoms placing at the ends of molecules: for all considered 1,n-dibromoalkanes, the hairpin conformers are more favorable than the all-trans ones.

Surface enhanced dynamic nuclear polarization solid-state NMR spectroscopy sheds light on Brønsted-Lewis acid synergy during the zeolite catalyzed methanol-to-hydrocarbon process.

After a prolonged effort over two decades, the reaction mechanism of the zeolite-catalyzed methanol-to-hydrocarbon (MTH) process is now well-understood: the so-called 'direct mechanism' (via direct coupling of two methanol molecules) is responsible for the formation of the initial carbon-carbon bonds, while the hydrocarbon pool (HCP)-based dual cycle mechanism is responsible for the formation of reaction products. While most of the reaction events occur at zeolite Brønsted acid sites, the addition of Lewis acid sites (i.e., via the introduction of alkaline earth cations like calcium) has been shown to inhibit the formation of deactivating coke species and hence increase the catalyst lifetime. With the aim to have an in-depth mechanistic understanding, herein, we employ magic angle spinning surface-enhanced dynamic nuclear polarization solid-state NMR spectroscopy to illustrate that the inclusion of Lewis acidity prevents the formation of carbene/ylide species on the zeolite, directly affecting the equilibrium between arene and olefin cycles of the HCP mechanism and hence regulating the ultimate product selectivity and catalyst lifetime.

Watching Bonds Move in a Large Antiaromatic Ring

In antiaromatic molecules, single and double bonds interconvert via a process called bond-shift valence tautomerization, which is often so fast that its rate is difficult to measure experimentally. In this issue of Chem, Wu and co-workers use dynamic NMR spectroscopy to study valence tautomerization in a giant antiaromatic macrocycle.

Character Table for Dirhenium Decacarbonyl of full non-rigid Molecule group (F-NRG)

Abstract: In this paper, we determine the character table for the full non-rigid molecule group (f-NRG) of Dirhenium Decacarbonyl. We showed that it is a molecule of group order 8, which can be written as (Z_2×Z_4), in which Z_2,Z_4 denotes cyclic groups of orders 2 and 4 respectively. We calculated the character table of the molecule using the package GAP which contains 8 conjugacy classes and 8 irreducible characters.

Inverted energy gap law for the nonradiative decay in fluorescent floppy molecules: larger fluorescence quantum yields for smaller energy gaps

The non-radiative decay of substituted dicyano-distyrylbenzenes in solution increase with the Franck–Condon energy, being opposite to the conventional energy gap law.