Instabilities across the isotropic conductivity point in a nematic phenyl benzoate under AC driving

We characterize the sequence of bifurcations generated by ac fields in a nematic layer held between unidirectionally rubbed ITO electrodes. The material, which possesses a negative dielectric anisotropy epsilona and an inversion temperature for electrical conductivity anisotropy sigmaa, exhibits a monostable tilted alignment near TIN, the isotropic-nematic point. On cooling, an anchoring transition to the homeotropic configuration occurs close to the underlying smectic phase. The field experiments are performed for (i) negative sigmaa and homeotropic alignment, and (ii) weakly positive sigmaa and nearly homeotropic alignment. Under ac driving, the Freedericksz transition is followed by bifurcation into various patterned states. Among them are the striped states that seem to belong to the dielectric regime and localized hybrid instabilities. Very significantly, the patterned instabilities are not excited by dc fields, indicating their possible gradient flexoelectric origin. The Carr-Helfrich mechanism-based theories that take account of flexoelectric terms can explain the observed electroconvective effects only in part.     

Polarization and interactions of colloidal particles in ac electric fields

Micrometer-sized polystyrene particles form two-dimensional crystals in alternating current (ac) electric fields. The induced dipole-dipole interaction is the dominant force that drives this assembly. We report measurements of forces between colloidal particles in ac electric fields using optical tweezers and find good agreement with the point dipole model. The magnitude of the pair interaction forces depends strongly on the bulk solution conductivity and decreases as the ionic strength increases. The forces also decrease with increasing field frequency. The salt and frequency dependences are consistent with double layer polarization with a characteristic relaxation frequency omega(CD) approximately a(2)/D, where a is the particle radius and D is the ion diffusivity. This enables us to reinterpret the order-disorder transition reported for micrometer-sized polystyrene particles [Lumsdon et al., Langmuir 20, 2108 (2004)], including the dependence on particle size, frequency, and ionic strength. These results provide a rational framework for identifying assembly conditions of colloidal particles in ac fields over a wide range of parameters.     

Temperature and pressure dependence of alanine dipeptide studied by multibaric-multithermal molecular dynamics simulations

We applied the multibaric-multithermal (MUBATH) molecular dynamics (MD) algorithm to an alanine dipeptide in explicit water. The MUBATH MD simulation covered a wide range of conformational space and sampled the states of PII, C5, alphaR, alphaP, alphaL, and C7(ax). On the other hand, the conventional isobaric-isothermal simulation was trapped in local-minimum free-energy states and sampled only a few of them. We calculated the partial molar enthalpy difference DeltaH and partial molar volume difference DeltaV among these states by the MUBATH simulation using the AMBER parm99 and AMBER parm96 force fields and two sets of initial conditions. We compared these results with those from Raman spectroscopy experiments. The Raman spectroscopy data of DeltaH for the C5 state against the PII state agreed with both MUBATH data with the AMBER parm96 and parm99 force fields. The partial molar enthalpy difference DeltaH for the alphaR state and the partial molar volume difference DeltaV for the C5 state by the Raman spectroscopy agreed with those for the AMBER parm96 force field. On the other hand, DeltaV for the alphaR state by the Raman spectroscopy was consistent with our AMBER-parm99 force-field result. All the experimental results fall between those of simulations using AMBER parm96 and parm99 force fields, suggesting that the ideal force-field parameters lie between those of AMBER parm96 and parm99.     

Electroconformational coupling (ECC): An electric field induced enzyme oscillation for cellular energy and signal transductions

Previous work has shown that membrane ATPases can extract free energy from applied oscillating electric fields for doing chemical work, e.g. to synthesize ATP from ADP and P_i or to transport Rb and Na ions against their respective electrochemical gradient. Data of these experiments are briefly reviewed. Electroconformational Coupling (ECC) is used to interpret these results. Computer analysis of a four state cyclic enzyme mechanism reproduces many experimental features. It is shown that a coulombic interaction between an enzyme and an alternating electric field (ac) can cause the enzyme to oscillate between different conformational states. If the frequency of the applied field matches the kinetic characteristics of the system and the amplitude matches the energy level required for inducing productive catalytic cycling, a phenomenological resonance between catalytic reaction and the periodic field is generated. A condition necessary for achieving energy coupling is the kinetic bias arising from the binding energy of the ligand. Analysis indicates that only dynamic electric fields, i.e. oscillating or fluctuating fields, can propel the cyclic reaction of the enzyme catalysis, and thus be effective for transducing energy. A stationary transmembrane electric field must be modulated, e.g. by opening and closing of an ion channel, to become oscillatory in order o produce the same effect. We propose that ECC is a fundamental process of cellular energy and signal transductions. Here, many membrane associated events are reduced to Michaelis-Menten types of enzyme catalytic reactions and they are thus amenable to the quantitative analysis of chemical kinetics.     

Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide

Non‐equilibrium molecular dynamics simulations of a solvated 21‐residue polyalanine (A21) peptide, featuring a high propensity for helix formation, have been performed at 300 K and 1 bar in the presence of external electromagnetic (e/m) fields in the microwave region (2.45 GHz) and an r.m.s. electric field intensity range of 0.01–0.05 V/Å. To investigate how the field presence affects transitions between the conformational states of a protein, we report 16 independent 40 ns‐trajectories of A21 starting from both extended and fully folded states. We observe folding‐behavior of the peptide consistent with prior simulation and experimental studies. The peptide displays a natural tendency to form stable elements of secondary structure which are stabilized by tertiary interactions with proximate regions of the peptide. Consistent with our earlier work, the presence of external e/m fields disrupts this behavior, involving a mechanism of localized dipolar alignment which serves to enhance intra‐protein perturbations in hydrogen bonds (English, et al., J. Chem. Phys. 2010 , 133, 091105), leading to more frequent transitions between shorter‐lifetime states. © 2012 Wiley Periodicals, Inc.     

Time-dependent density functional theory investigation of electric field effects on absorption spectra of meso-meso-linked zinc porphyrin arrays: Role of charge-transfer States

By using time-dependent density functional theory, we calculated the transition energies of a zinc porphyrin monomer and its meso-meso-linked arrays. In line with the prediction of the molecular exciton model, the calculated splitting energy of the Soret band increased as the number of linked porphyrins increased. We then examined how the transition energies of the dimer array were shifted by an applied electric field. For reproduction of an electroabsorption spectrum (EA), i.e., the field-induced change in absorption intensity, a model Hamiltonian constructed from five states is proposed. It is concluded for the dimer that the field-induced coupling between the lower-energy Soret band Se and the lower-lying ionic character (charge-transfer) states is responsible for the experimentally observed blue shift of Se as well as the second-derivative profile in the EA spectrum.     

Rotationally resolved magnetic vibrational circular dichroism of the paramagnetic molecule NO

Magnetic vibrational circular dichroism (MVCD) enables the measurement of molecular magnetic moments with modest spectral resolution. Due to its paramagnetism, NO gives a much stronger spectral response, about 3 orders of magnitude more intense, than do typical diamagnetic molecules. The molecule thus provides a convenient test for the experiment and theory of paramagnetic rotors. We have measured and analyzed the MVCD, equivalent to the molecular Zeeman spectra, of NO in co-linear magnetic fields of 0.1, 0.2, 2, 4 and 8 Tesla. Similar MVCD intensities were observed for both the (2)Π(1/2) and (2)Π(3/2) components of NO, particularly for high J values, which demonstrates a considerable deviation from pure Hund's case (a) for NO. The g(J)-values for the (2)Π(1/2) components of NO, which can be determined from our experimental spectra by moment analysis, agree well with the predicted values from Radford's theory. For the (2)Π(3/2) components, we tested this theory by simulating the MVCD and absorption spectra, and comparing them with our experimental spectra by use of moment analysis to show that they match well in terms of magnetic properties. While 0.2 T experiments easily develop sufficient MVCD for analysis of NO spectra and these low field intensities have a linear field dependence, spectra in the strong fields accessible in our study showed non-linear response due to onset of saturation effects. We also observed a strong field dependence for the absorption intensities for some (2)Π(3/2) components that was not encompassed in the theoretical model. Finally, a full coupling scheme provided analytical MVCD and absorption intensities that were in good agreement with the experimental values.     

Nonlinear ac responses of electro-magnetorheological fluids

We apply a Langevin model to investigate the nonlinear ac responses of electro-magnetorheological (ERMR) fluids under the application of two crossed dc magnetic (z axis) and electric (x axis) fields and a probing ac sinusoidal magnetic field. We focus on the influence of the magnetic fields which can yield nonlinear behaviors inside the system due to the particles with a permanent magnetic dipole moment. Based on a perturbation approach, we extract the harmonics of the magnetic field and orientational magnetization analytically. To this end, we find that the harmonics are sensitive to the degree of anisotropy of the structure as well as the field frequency. Thus, it is possible to real-time-monitor the structure transformation of ERMR fluids by detecting the nonlinear ac responses.     

Systematic statistical comparison of comparative molecular similarity indices analysis molecular fields for computer-aided lead optimization

Comparative molecular similarity indices analysis (CoMSIA) is a 3D quantitative structure-activity relationship technique used to determine structural and electronic features influencing biological activity. This proves particularly useful for facilitating lead optimization projects. This study aimed to compare CoMSIA models produced using different subsets of the CoMSIA molecular fields (steric, electrostatic, hydrophobic, hydrogen-bond donor, and hydrogen-bond acceptor) in a systematic and statistically valid manner. A total of 23 data sets sourced from the literature were used to compare molecular field contribution and model predictivity using leave-one-out cross-validated R2 values. Predictive ability varied in a highly statistically significant manner depending on the set of CoMSIA molecular fields used. In general, the greater the number of CoMSIA molecular fields included in the analysis, the better the model predictivity was. There is great redundancy in the information contained in the different CoMSIA molecular fields. When all five CoMSIA molecular fields are included, the hydrophobic and electrostatic fields had the largest and the steric field the smallest contribution. Data sets were clustered into four groups on the basis of the utility of molecular field sets to generate predictive models.     

Electric-field-induced dissociation of heavy Rydberg ion-pair states

A classical trajectory Monte Carlo approach is used to simulate the dissociation of H(+)???F(-) and K(+)???Cl(-) heavy Rydberg ion pairs induced by a ramped electric field, a technique used experimentally to detect and probe ion-pair states. Simulations that include the effects of the strong short-range repulsive interaction associated with ion-pair scattering are in good agreement with experimental results for Stark wavepackets probed by a ramped field, demonstrating that many of the characteristics of field-induced dissociation can be well described using a quasi-classical model. The data also show that states with a given value of principal quantum number (i.e., binding energy) can dissociate over a broad range of applied fields, the exact field being governed by the initial orbital angular momentum and orientation of the state.     

Calculated properties of the active site of oxidized rubredoxins

For a molecular model of the Fe-S active site complex in oxidized rubredoxin, we have calculated the spin-orbit coupling between the ground sextet state and excited quartet and doublet states which gives rise to the observed zero field splitting of the sextet ground state into three spin-mixed Kramers doublets. Additionally, we have used the six spin-mixed sextet state components to calculate effective magnetic moments, magnetic field energies and nine g values corresponding to transitions between the three pairs of Kramers doublets in applied magnetic fields along three perpendicular axes. We have calculated these properties for eight conformational variations of the ligands around the Fe at the active site. The results of these calculations clearly show the origin of the observed g=4.3 signal previously described only in terms of the phenomenological spin-Hamiltonian formalism. For the eight conformations considered, five have this characteristic signal. Zero field splitting comparable to the observed values could be obtained for all symmetries studied. In addition, the calculated values of magnetic moment in all symmetries correspond to that of high spin ferric ion and do not vary appreciably with temperature above 77° K, in agreement with experimental results. From comparison of all our calculated results with experiment, it appears that the active site in oxidized rubredoxins could have small conformational variations in different rubredoxins and under the various experimental conditions used.     

Evidence for genotoxic effects of resonant ELF magnetic fields

The possibility that extremely low frequency (ELF) magnetic fields affect the genomic integrity of the cell is the objective of this study. Human peripheral lymphocytes (HPLs) were exposed to different exposure conditions combining ac and static magnetic fields. We used the micronuclei (MN) cytogenetic technique, because MN formation is considered as a marker of chromosomal damage produced by genotoxic agents.The first set of experiments were performed at 50 Hz, 150 μT rms and 32 Hz, 75 μT and 150 μT rms magnetic fields with the static geomagnetic field components nulled. No effects were detected using the MN test on HPL as an indicator for cellular genomic damage when the static magnetic field was nulled. Moreover, such exposure to an ac magnetic field does not appear to interfere with the action of a powerful genotoxic agent mytomicin-C (MMC), i.e. there was no synergistic effect.The second set of experiments were conducted exposing cells to 32 Hz, 150 μT and 75 μT rms, parallel to a 42 μT dc magnetic field. The 75 μT rms, 32 Hz exposure condition was chosen to maximize the resonance effect on Ca²⁺ according to parametric resonance theory. We found a statistically significant increase of MN for both exposure conditions. This experiment provides evidence for the genotoxic effects of resonant ELF magnetic fields in human lymphocytes.     

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.     

Reference-Quality Free Energy Barriers in Catalysis from Machine Learning Thermodynamic Perturbation Theory

For the first time, we report calculations of the free energies of activation of cracking and isomerization reactions of alkenes that combine several different electronic structure methods with molecular dynamics simulations. We demonstrate that the use of a high level of theory (here Random Phase Approximation—RPA) is necessary to bridge the gap between experimental and computed values. These transformations, catalyzed by zeolites and proceeding via cationic intermediates and transition states, are building blocks of many chemical transformations for valorization of long chain paraffins originating, e.g., from plastic waste, vegetable oils, Fischer–Tropsch waxes or crude oils. Compared with the free energy barriers computed at the PBE+D2 production level of theory via constrained ab initio molecular dynamics, the barriers computed at the RPA level by the application of Machine Learning thermodynamic Perturbation Theory (MLPT) show a significant decrease for isomerization reaction and an increase of a similar magnitude for cracking, yielding an unprecedented agreement with the results obtained by experiments and kinetic modeling.     

Molecular wave packet interferometry and quantum entanglement

We study wave packet interferometry (WPI) considering the laser pulse fields both classical and quantum mechanically. WPI occurs in a molecule after subjecting it to the interaction with a sequence of phase-locked ultrashort laser pulses. Typically, the measured quantity is the fluorescence of the molecule from an excited electronic state. This signal has imprinted the interference of the vibrational wave packets prepared by the different laser pulses of the sequence. The consideration of the pulses as quantum entities in the analysis allows us to study the entanglement of the laser pulse states with the molecular states. With a simple model for the molecular system, plus several justified approximations, we solve for the fully quantum mechanical molecule-electromagnetic field state. We then study the reduced density matrices of the molecule and the laser pulses separately. We calculate measurable corrections to the case where the fields are treated classically.     

Molecular dynamics simulations of structure and dynamics of organic molecular crystals

A set of model compounds covering a range of polarity and flexibility have been simulated using GAFF, CHARMM22, OPLS and MM3 force fields to examine how well classical molecular dynamics simulations can reproduce structural and dynamic aspects of organic molecular crystals. Molecular structure, crystal structure and thermal motion, including molecular reorientations and internal rotations, found from the simulations have been compared between force fields and with experimental data. The MM3 force field does not perform well in condensed phase simulations, while GAFF, CHARMM and OPLS perform very similarly. Generally molecular and crystal structure are reproduced well, with a few exceptions. The atomic displacement parameters (ADPs) are mostly underestimated in the simulations with a relative error of up to 70%. Examples of molecular reorientation and internal rotation, observed in the simulations, include in-plane reorientations of benzene, methyl rotations in alanine, decane, isopropylcyclohexane, pyramidal inversion of nitrogen in amino group and rotation of the whole group around the C-N bond. Frequencies of such dynamic processes were calculated, as well as thermodynamic properties for reorientations in benzene and alanine. We conclude that MD simulations can be used for qualitative analysis, while quantitative results should be taken with caution. It is important to compare the outcomes from simulations with as many experimental quantities as available before using them to study or quantify crystal properties not available from experiment.     

Laser field induced charge transfer: Para-nitroaniline coupled to a quantum mechanical radiation field

Summary We present a preliminary model for describing a solvated intramolecular charge transfer reaction coupled to a quantum mechanical radiation field. Actual calculations of energies and couplings were performed with a recently developed self-consistent reaction field response method. The representation of dressed molecular states is used for calculating state populations for various laser fields. The state populations are sensitive to the properties of the laser field.     

How to compare diffusion processes assessed by single-particle tracking and pulsed field gradient nuclear magnetic resonance

Heterogeneous diffusion processes occur in many different fields such as transport in living cells or diffusion in porous media. A characterization of the transport parameters of such processes can be achieved by ensemble-based methods, such as pulsed field gradient nuclear magnetic resonance (PFG NMR), or by trajectory-based methods obtained from single-particle tracking (SPT) experiments. In this paper, we study the general relationship between both methods and its application to heterogeneous systems. We derive analytical expressions for the distribution of diffusivities from SPT and further relate it to NMR spin-echo diffusion attenuation functions. To exemplify the applicability of this approach, we employ a well-established two-region exchange model, which has widely been used in the context of PFG NMR studies of multiphase systems subjected to interphase molecular exchange processes. This type of systems, which can also describe a layered liquid with layer-dependent self-diffusion coefficients, has also recently gained attention in SPT experiments. We reformulate the results of the two-region exchange model in terms of SPT-observables and compare its predictions to that obtained using the exact transformation which we derived.     

A QM/MM approach to interpreting 67Zn solid-state NMR data in zinc proteins

We present here a (67)Zn solid-state NMR investigation of Zn(2+) substituted rubredoxin. The sample has been prepared as both a dry powder and a frozen solution to determine the effects of static disorder on the NMR line shape. Low-temperature experiments have been performed at multiple fields to determine the relative contributions to the NMR line shape from the electric field gradient and the anisotropic shielding tensors. Finally we present the theoretical interpretation of the experimental results utilizing a combined quantum mechanical molecular mechanics (QM/MM) approach. Theory predicts a sizable contribution from anisotropic shielding as compared with previously examined model systems. This is in good agreement with the experimental data.     

Phase behavior of polarizable spherocylinders in external fields

Applied electric fields are known to induce significant changes in the properties of systems of polarizable molecules or particles. For rod-shaped molecules, the field-induced behavior can be rather surprising, as in the case of the negative electric birefringence of concentrated solutions of rodlike polyelectrolytes. We have investigated the interplay of shape anisotropy and field-induced anisotropy in molecular dynamics simulations of systems of polarizable soft spherocylinders in an electric field, in the limit of infinitely anisotropic polarizability, taking full account of mutual induction effects. We find a novel crystalline structure (K(2)) in the high-field limit, whose formation is driven by interactions between induced dipoles. For high pressures, the phase diagram exhibits a polar nematic phase between the hexagonal close-packed crystal phase and the K(2) phase. We also compare this system with an analogous system of spherocylinders with permanent electric dipoles and find that qualitatively similar behavior is obtained in the limit of strong coupling of the permanent dipoles to the external field.