Conformational Slippage Determines Rotational Frequency in Five‐Component Nanorotors

Several five‐component nanorotors ROT‐3 that rotate at different rates were prepared by adding phenanthrolines of distinct lateral size as brake blocks to the four‐component nanorotor ROT‐2. The brake blocks interfere with the 180° rotor causing the rotational frequency to drop from 97 kHz to 5 kHz. The effect of the rotating brake blocks on the rotational frequency in ROT‐3 is accurately predicted by a nanomechanical model called “conformational slippage”. For quantification, the interaction of the brake blocks with the trajectory of the main rotator is gauged based on the number of interfering vs. non‐interfering conformations as computed by PM6.     

Intramolecular Hydrogen Bonding Restricts Gd–Aqua‐Ligand Dynamics

Aqua ligands can undergo rapid internal rotation about the M−O bond. For magnetic resonance contrast agents, this rotation results in diminished relaxivity. Herein, we show that an intramolecular hydrogen bond to the aqua ligand can reduce this internal rotation and increase relaxivity. Molecular modeling was used to design a series of four Gd complexes capable of forming an intramolecular H‐bond to the coordinated water ligand, and these complexes had anomalously high relaxivities compared to similar complexes lacking a H‐bond acceptor. Molecular dynamics simulations supported the formation of a stable intramolecular H‐bond, while alternative hypotheses that could explain the higher relaxivity were systematically ruled out. Intramolecular H‐bonding represents a useful strategy to limit internal water rotational motion and increase relaxivity of Gd complexes.     

Current-induced rotation of helical molecular wires

We show that electric current running through a nanojunction with a biased helical molecule can induce unidirectional rotation of the molecular component. In an electric field, conduction electrons injected into the molecule are accelerated along the helical path going through its body, thereby gaining directed angular momentum. Conservation laws require that an angular momentum of the same size but opposite sense is imparted to the rigid-body rotation of the helix. We describe the angular momentum exchange processes that underlie the operation of the nanorotor, discuss factors limiting its efficiency, and propose potential applications.     

Elimination of translational and rotational motions in nuclear orbital plus molecular orbital theory

The nuclear orbital plus molecular orbital (NOMO) theory was developed in order to determine the nonadiabatic nuclear and electronic wave functions. This study presents a formulation to remove the contamination of rotational motion as well as translational motion in the NOMO theory. We have formulated the translation- and rotation-free (TRF)-NOMO theory by introducing the TRF Hamiltonian. The principal moment of inertia, which is the denominator in the rotational Hamiltonian, is expanded in a Taylor series. The zeroth-order of the Taylor expansion corresponds to a rigid-body rotator. The first-order terms contribute the coupling between the vibration and the rotation. Hartree-Fock equations have been derived in the framework of the TRF-NOMO theory. Numerical assessments, which were preformed for H2, D2, T2, mu2 (muon dimmer), and H2O, confirmed the importance of the TRF treatment.     

Ionization dynamics of a water dimer: specific reaction selectivity

Ionization dynamics of a water dimer have been investigated by means of a direct ab initio molecular dynamics (MD) method. Two electronic state potential energy surfaces of (H(2)O)(2)(+) (ground and first excited states, (2)A' and (2)A') were examined as cationic states of (H(2)O)(2)(+). Three intermediate complexes were found as product channels. One is a proton transfer channel where a proton of H(2)O(+) is transferred into the H(2)O and then a complex composed of H(3)O(+)(OH) was formed. The second is a face-to-face complex channel denoted by (H(2)O-OH(2))(+) where the oxygen-oxygen atoms directly bind each other. Both water molecules are equivalent to each other. The third one is a dynamical complex where H(2)O(+) and H(2)O interact weakly and vibrate largely with a large intermolecular amplitude motion. The dynamics calculations showed that in the ionization to the (2)A' state, a proton transfer complex H(3)O(+)(OH) is only formed as a long-lived complex. On the other hand, in the ionization to the (2)A' state, two complexes, the face-to-face and dynamical complexes, were found as product channels. The proton of H(2)O(+) was transferred to H(2)O within 25-50 fs at the (2)A' state, meaning that the proton transfer on the ground state is a very fast process. On the other hand, the decay process on the first excited state is a slow process due to the molecular rotation. The mechanism of the ionization dynamics of (H(2)O)(2) was discussed on the basis of theoretical results.     

Further insight into the relaxation dynamics of photoexcited I-(H2O)n clusters

First-principles molecular dynamics simulations of the excited-state dynamics of I-(H2O)3 have been performed to gain some insight into the general features of the relaxation process of photoexcited I-(H2O)n clusters. The relaxation of excited I-(H2O)3 is characterized by rapid motion of water molecules and slow recoil motion of the iodine atom. Both solvent reorganization and iodine atom motion appear to be important for interpreting the existing femtosecond photoelectron spectroscopy experimental results.     

Pulsed field ionization-ZEKE spectroscopy of cresoles and their aqueous complexes: internal rotation of methyl group and intermolecular vibrations

Pulsed field ionization-ZEKE photoelectron spectroscopy and (1 + 1) R2PI spectroscopy have been applied to the cis- and trans-m-cresol.H2O clusters. The internal rotational structure in the S1 state has been re-assigned, and the potential curve has been determined for the cluster. The PFI-ZEKE spectra of the cis- and trans-isomers show low-frequency bands up to 1000 cm-1 above the adiabatic ionization potential IP0. The low-frequency bands are assigned to the internal rotation of the methyl group, the intermolecular stretching and their combination bands in the m-cresol.H2O cluster cation. Level energies and relative transition intensities are reproduced well by a one-dimensional rotor model with a three-fold axis potential. Potential curves for the internal rotation have been determined for both cis- and trans-isomers of m-cresol.H2O cations. The effect of the cluster formation upon the internal methyl rotation, and the interaction between the methyl rotation and the intermolecular vibration are discussed.     

Guests Like Gear Levers: Donor Binding to Coordinatively Unsaturated Metal Sites in MIL-101 Controls the Linker′s Rotation

We present investigation of the effect of electron-donor guests on framework mobility in the metal–organic framework (MOF) MIL-101(Cr) monitored by solid state ²H NMR spectroscopy. In a guest-free material, the mobile phenylene fragments of the terephthalate (TP) linkers populate two fractions with notably different kinetic parameters for torsional motion. Two fractions of rotational motion are indicative of non-equivalence of TP linker binding to the Cr₃O trimer, the primary building unit of the MIL-101 framework. It is established that the interaction of the guest molecules with coordinatively unsaturated metal sites (CUS) of the MOF dramatically decreases torsional barriers for the linker motions, enhancing the rotation rate. This result is opposite to a more conventional slowing down effect on the linker rotation of the guests not selectively interacting with the adsorption sites inside the framework of the MOFs. The effect of coordination on both the torsional barrier and the rotation rate depends notably on the particular guest interacting with the CUS. The found effects of the guest on the rotational motion represent a basis for developing the strategy for ruling and controlling the linker rotation in MOFs with CUS. It is shown that if water occupies CUS, another guest (tert-butanol, cyclohexanone) fails to competitively coordinate to the site.     

An intrinsic reaction coordinate calculation of the torsion-internal rotation potential of hydrogen peroxide and its isotopomers

Intrinsic reaction coordinate (IRC) calculations of the internal rotation (torsional) potentials for H(2)O(2) and its isotopomers HDO(2) and D(2)O(2) were carried out at the CCSD(T)/CBS//aug-cc-pVDZ level. Two extrapolation methods were used to obtain energies in the complete basis set (CBS) limit. The full IRC potential was constructed from scans from the C(2v) (cis) and C(2h) (trans) transition states to the equilibrium C(2) (gauche) structure. The IRC potential for H(2)O(2) was fit to a five-term Fourier function; coefficients were compared with values obtained from spectroscopic data. The twofold IRC torsional potentials were used to obtain torsional eigenvalues, which yielded values of the transitions between various ntau states. These results compare favorably with Raman and near-infrared data. Our calculations provide values of the cis and trans barriers of 2495 and 364 cm(-1), respectively, which are in good agreement with both previously calculated and experimentally derived values. It appears that coupling between torsional motion and other degrees of freedom is not significant in these molecules.     

Validity of phase space theory for atom-diatom insertion reactions

Phase space theory (PST) is applied to the calculation of state-resolved integral and differential cross sections for the complex-forming atom-diatom insertion reactions A + H(2) --> AH(2) --> AH + H with A = C((1)D), S((1)D), O((1)D), and N((2)D). In the asymptotic channels, vibration motion is quantized while rotation and translation motions are treated classically. The approach is compared to exact quantum scattering calculations and quantum statistical models. Given the simplicity of PST, the agreement with the previous much more refined treatments is very satisfying. Although PST is a well-established theory, this work is, to our knowledge, the first such systematic comparison of its predictions with accurate quantum scattering and quantum statistical calculations.     

Direct dynamics simulations using Hessian-based predictor-corrector integration algorithms

In previous research [J. Chem. Phys. 111, 3800 (1999)] a Hessian-based integration algorithm was derived for performing direct dynamics simulations. In the work presented here, improvements to this algorithm are described. The algorithm has a predictor step based on a local second-order Taylor expansion of the potential in Cartesian coordinates, within a trust radius, and a fifth-order correction to this predicted trajectory. The current algorithm determines the predicted trajectory in Cartesian coordinates, instead of the instantaneous normal mode coordinates used previously, to ensure angular momentum conservation. For the previous algorithm the corrected step was evaluated in rotated Cartesian coordinates. Since the local potential expanded in Cartesian coordinates is not invariant to rotation, the constants of motion are not necessarily conserved during the corrector step. An approximate correction to this shortcoming was made by projecting translation and rotation out of the rotated coordinates. For the current algorithm unrotated Cartesian coordinates are used for the corrected step to assure the constants of motion are conserved. An algorithm is proposed for updating the trust radius to enhance the accuracy and efficiency of the numerical integration. This modified Hessian-based integration algorithm, with its new components, has been implemented into the VENUS/NWChem software package and compared with the velocity-Verlet algorithm for the H(2)CO-->H(2)+CO, O(3)+C(3)H(6), and F(-)+CH(3)OOH chemical reactions.     

Planar study of H2O+Cl<-->HO+HCl reactions

The first four dimensional (4D) quantum scattering calculations on the tetra-atomic H2O+Cl<-->HO+HCl reactions are reported. With respect to a full (6D) treatment, only the planar constraint and a fixed length for the HO spectator bond are imposed. This work explicitly accounts for the bending and local HO stretching vibrations in H2O, for the vibration of HCl and for the in-plane rotation of the H2O, HO and HCl molecules. The calculations are performed with the potential energy surface of Clary et al. and use a Born-Oppenheimer type separation between the motions of the light and the heavy nuclei. State-to-state cross sections are reported for a collision energy range 0-1.8 eV measured with respect to H2O+Cl. For the H2O+Cl reaction, present results agree with previous (3D) non planar calculations and confirm that excitation of the H2O stretching promotes more reactivity than excitation of the bending. New results are related to the rotation of the H2O molecule: the cross sections are maximal for planar rotational states corresponding to 10相似文献   

Multirotations of (Anilinium)([18]Crown‐6) Supramolecular Cation Structure in Magnetic Salt of [Ni(dmit)2]−

A solid‐state dynamic supramolecular structure consisting of (anilinium)([18]crown‐6) was arranged as the cation in a salt of [Ni(dmit)₂]^? (dmit=2‐thioxo‐1,3‐dithiole‐4,5‐dithiolate). With the ammonium moiety of anilinium located within the cavity of [18]crown‐6, a hydrogen‐bonded supramolecular structure is formed, with an orthogonal arrangement between the π plane of anilinium and the mean O6 plane of [18]crown‐6. In this supramolecular cation, both anilinium and [18]crown‐6 act as dynamic units with different rotational modes in the solid state. The uniform stacks of cations form an antiparallel arrangement, thus producing a layer structure. Sufficient space for the 180° flip‐flop motion of the phenyl ring and the rotation of [18]crown‐6 was observed in the cation layer. Thermally activated 180° flip‐flop motions, with a frequency of 6 MHz at room temperature and an activation energy of 31 kJ mol^?1, were confirmed by temperature‐dependent ²H NMR spectra of ([D₅]anilinium)‐([18]crown‐6)[Ni(dmit)₂]. A double‐minimum potential for the molecular rotation of anilinium, with a barrier of approximately 40 kJ mol^?1, was indicated by ab initio calculations. The wide‐line ¹H NMR spectra indicated a thermally activated rotation of [18]crown‐6 at temperatures above 250 K. Therefore, multiple molecular motions of the 180° flip‐flop motion of the phenyl ring and the rotation of [18]crown‐6 occur simultaneously in the solid state. The temperature‐dependent dielectric constants revealed that the molecular motion of [18]crown‐6, other than the flip‐flop motion, dominates the dielectric response in the measured temperature and frequency range.     

Proline zwitterion dynamics in solution, glass, and crystalline state

Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.     

Intramolecular Hydrogen Bonding Restricts Gd–Aqua-Ligand Dynamics

Aqua ligands can undergo rapid internal rotation about the M−O bond. For magnetic resonance contrast agents, this rotation results in diminished relaxivity. Herein, we show that an intramolecular hydrogen bond to the aqua ligand can reduce this internal rotation and increase relaxivity. Molecular modeling was used to design a series of four Gd complexes capable of forming an intramolecular H-bond to the coordinated water ligand, and these complexes had anomalously high relaxivities compared to similar complexes lacking a H-bond acceptor. Molecular dynamics simulations supported the formation of a stable intramolecular H-bond, while alternative hypotheses that could explain the higher relaxivity were systematically ruled out. Intramolecular H-bonding represents a useful strategy to limit internal water rotational motion and increase relaxivity of Gd complexes.     

Internal rotation in molecular complexes: some problems concerning the evaluation of equilibrium and rate constants

The conventional one-term partition function of free internal rotation (so far the only means used in the literature for evaluation of the thermodynamics of this motion) shows incorrect limit behavior for low temperatures and/or small values of reduced moments of inertia. This situation is particularly pertinent to van der Waals molecules and hydrogen bonded systems. Consequences of the application of the newly suggested improved formulae for the heat content function, entropy, and heat capacity have been analyzed for (H₂)₂, (N₂)₂, ClF.HF, HF.ClF, HCN.HCl, HCN.DCl, (H₂O)₂, CF₃H.OH₂, CCl₃H.OH₂, and cyclopropane.H₂O. Considerable changes in the values of thermodynamic or kinetic characteristics of the systems have been found when applying the new formulae. Relations to the results available with the exact partition function of the free internal rotation have been analyzed. Consequences of the new approach for the recently performed theoretical evaluation of anesthetic activity based on the conventional formula are briefly discussed.Dedicated to Professor Camille Sandorfy on the occasion of his 65th birthdayPart XXVII in the series Multi-Molecular Clusters and Their Isomerism; Part XXVI, see [52]     

Syntheses and characterization of oxygen/sulfur-bridged incomplete cubane-type clusters, [Mo3S4Tp3]+ and [Mo3OS3Tp3]+, and a mixed-metal cubane-type cluster, [Mo3FeS4ClTp3]. X-ray structures of [Mo3S4Tp3]Cl, [Mo3OS3Tp3]PF6, and [Mo3FeS4ClTp3

The reaction of [Mo3S4(H2O)9]4+ (1) with hydrotris(pyrazolyl)borate (Tp) ligands produced [Mo3S4Tp3]Cl x 4 H2O ([3]Cl x 4 H2O) in an excellent yield. An X-ray structure analysis of [3]Cl x 4 H2O revealed that each molybdenum atom bonded to the Tp ligand. We report four salts of 3, [3]Cl x 4 H2O, [3]tof x 2 H2O, [3]PF6 x H2O, and [3]BF4 x 2 H2O in this paper. The solubility and stability of the chloride salt in organic solvents differ completely from those of the other salts. We have also prepared a new compound, [Mo3OS3Tp3]PF6 x H2O ([4]PF6 x H2O), via the reaction of [Mo3OS3(H2O)9]4+ (2) with KTp in the presence of NH4PF6. All the molybdenum atoms bonded to Tp ligand. 1H NMR signals corresponding to nine protons bonded to three pyrazole rings in one Tp were observed in a spectrum (at 253 K) of [3]BF4 x 2 H2O. It shows that cluster 3 has a 3-fold rotation axis in CD2Cl2 solution. Twenty-one 1H NMR signals corresponding to twenty-seven protons bonded to nine pyrazole rings in three Tp ligands were observed in a spectrum (at 233 K) of [4]PF6 x H2O; obviously, 4 has no 3-fold rotation axis, in contrast to 3. The short CH...mu3S distance caused large upfield chemical shifts in the 1H NMR spectra of 3 and 4. The reaction of 3 with metallic iron in CH2Cl2 produced [Mo3FeS4XTp3] (X = Cl (5), Br (6)). X-ray structure analysis of 5 has revealed the existence of a cubane-type core Mo3FeS4. Complex 3 functions as a metal-complex ligand for preparing a novel mixed-metal complex even in nonaqueous solvents. The cyclic voltammogram of 5 shows two reversible one-electron couples (E(1/2) = -1.40 and 0.52 V vs SCE) and two irreversible one-electron oxidation processes (E(pc) = 1.54 and 1.66 V vs SCE).     

Vibrational analysis of the H5O2+ infrared spectrum using molecular and driven molecular dynamics

Standard molecular and driven molecular dynamics are used to analyze prominent spectral features in the H5O2+ infrared spectrum. In the driven method, the molecular Hamiltonian is augmented with a time-dependent term, mu x epsilon(0) sin(omegat), where mu is the dipole moment of H5O2+, epsilon0 is the electric field, and omega is the frequency. The magnitude of the electric field determines whether the driving is mild (the harmonic limit) or strong (anharmonic motion and mode coupling). We analyze the spectrum in the wavenumber range from 600 to 1900 cm(-1), where recent experimental measurements are available for H5O2+. On the basis of the simulations, we have assigned the broad feature around 1000 cm(-1) to the proton transfer coupled with the torsion motion. Intense absorption near 1780 cm(-1) is assigned to the H2O monomer bend coupled with proton transfer.     

Reaction dynamics simulations of the identity S(N)2 reaction H(2)O + HOOH(2)(+)--> H(2)OOH(+)+ H(2)O. Requirements for reaction and competition with proton transfer

Despite the fact that the transition structure of the gas phase S(N)2 reaction H(2)O + HOOH(2)(+)--> HOOH(2)(+)+ H(2)O is well below the reactants in potential energy, the reaction has not yet been observed by experiment. Variational transition state RRKM theory reveals a strong preference for the competing proton transfer reaction H(2)O + HOOH(2)(+)--> H(3)O(+)+ HOOH due to entropy factors. Born-Oppenheimer reaction dynamics simulations confirm these results. However, by increasing the collision energy to around 7.5 eV the probability for nucleophilic substitution increases relative to proton transfer. These observations are explained by the presence of the key common intermediate HOO(H)[dot dot dot]H-OH(2)(+) which leads to effective proton transfer, but can be avoided with increasing collision energy. However, the S(N)2 probability remains below 0.2 since successful passage through the TS requires optimum initial orientation of the reactants, excitation of the relative translational motion and good phase correlation between the O-O vibration and the motion of the incoming water.     

4,4′‐Tri­methyl­enedipyridinium bis­[carboxy­methyl­phos­pho­nate(1–)]: a three‐dimensional framework structure built from O—H⃛O,N—H⃛O and C—H⃛O hydrogen bonds

In the title compound, C₁₃H₁₆N₂²⁺·2C₂H₄O₅P⁻, the cation lies across a twofold rotation axis in space group Fdd2. The anions are linked into molecular ladders by two O—H⃛O hydrogen bonds [H⃛O = 1.73 and 1.77 Å, O⃛O = 2.538 (2) and 2.598 (3) Å, and O—H⃛O = 160 and 170°], these ladders are linked into sheets by a single type of N—H⃛O hydrogen bond [H⃛O = 1.75 Å, N⃛O = 2.624 (3) Å and N—H⃛O = 171°] and the sheets are linked into a three‐dimensional framework by a single type of C—H⃛O hydrogen bond [H⃛O = 2.48 Å, C⃛O = 3.419 (4) Å and C—H⃛O = 167°].