Laser-operated chiral molecular switch: quantum simulations for the controlled transformation between achiral and chiral atropisomers

We report quantum dynamical simulations for the laser controlled isomerization of 1-(2-cis-fluoroethenyl)-2-fluorobenzene based on one-dimensional electronic ground and excited state potentials obtained from (TD)DFT calculations. 1-(2-cis-fluoroethenyl)-2-fluorobenzene supports two chiral and one achiral atropisomers, the latter being the most stable isomer at room temperature. Using a linearly polarized IR laser pulse the molecule is excited to an internal rotation around its chiral axis, i.e. around the C-C single bond between phenyl ring and ethenyl group, changing the molecular chirality. A second linearly polarized laser pulse stops the torsion to prepare the desired enantiomeric form of the molecule. This laser control allows the selective switching between the achiral and either the left- or right-handed form of the molecule. Once the chirality is "switched on" linearly polarized UV laser pulses allow the selective change of the chirality using the electronic excited state as intermediate state.     

Effect of torsional potential on the predicted phase behavior of n-alkanes

The effect of torsional potential on the predictions of simulation for vapor–liquid equilibria of n-alkanes is determined. Calculations are performed with histogram-reweighting Monte Carlo simulations in the grand canonical ensemble. Decreasing the magnitude of energy barriers to dihedral rotation or allowing free rotation is found to have no effect on the predicted vapor–liquid equilibria. Restriction of the dihedral angles to a Gaussian distribution around the minimum energy conformation causes an under-prediction of the liquid densities and critical temperatures by a maximum of 7% and 2%, respectively, with discrepancies increasing monotonically with the number of dihedral angles present in a molecule. No significant deviation in vapor pressure is observed for any compound, regardless of torsional potential used. An analysis of the conformational behavior reveals that restriction of the dihedral sampling has a measurable effect on excluded volume of the molecule, and this change of conformational behavior is responsible for the reduction in the predicted saturated liquid densities observed in this work. Similar calculations for force fields employing reduced dihedral potentials or freely jointed chains show little change in the predicted excluded volume compared to the reference force field.     

Role of short-range electrostatics in torsional potentials

A force field needs to decide if it should contain a torsional potential or not. A helpful guide to this decision should come from a quantum mechanical energy partitioning. Here we analyze the energy profiles of eight simple molecules (ethane, hydrogen peroxide, hydrazine, methanol, acetaldehyde, formamide, acetamide and N-methylacetamide) subject to rotation around a torsion angle. Coulomb interaction energies between all atom pairs in a molecule are monitored during the rotation. Atoms are defined as finite electron density fragments by quantum chemical topology, a method that enables well-defined short-range interactions (1-2, 1-3 and 1-4). Energy profiles of Coulomb interaction energies mostly counteract the ab initio energy profiles. This and future work strives to settle ambiguities in current force field design.     

Potential energy surfaces for van der waals complexes of rare gases with H2S and H2S2: Extension to xenon interactions and hyperspherical harmonics representation

This article is an account and extension of a series of recent investigations, which using extensive quantum chemical methods provide analytical hyperspherical representations of the potential energy surfaces for the interactions of rare gases with H₂S as a rigid molecule, and H₂S₂, considered as a floppy molecule with respect to torsional mode. For the H₂S‐rare gas systems, the representation is based on a minimal model, here introduced and discussed. For H₂S₂, the study of the interaction with Xe, not considered previously, completes the series. The results are discussed with reference to the properties and trends expected for interactions of van der Waals type. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Molecular dynamics investigation of bent-core molecules on a water surface

Molecular dynamics simulations are carried out for bent-core molecules at water surfaces. The water surface is shown to alter the equilibrium molecular structure significantly by causing a different class of torsional states to become more favorable. The equilibrium structure is also altered by the substitution of chlorine atoms for hydrogen atoms on the central phenyl ring in that this substitution forces the bent core to remain in a single torsional state rather than be delocalized among several torsional states. The consequences of these structural changes on the chirality and packing of these molecules on water surfaces are discussed.     

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

The intermolecular potentials for the NO(X 2Pi)-Kr and NO(A 2Sigma+)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1 2A' state [NO(X 2Pi)-Kr] and the multireference singles and doubles configuration interaction method for the excited 2 2A' state [NO(A 2Sigma+)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system.     

The influence of layer curvature on switching in ferroelectric B2 phases of liquid crystals having bent-shape molecules

In the B₂ phase of liquid crystalline compounds with bent-shape molecules ferroelectric switching can occur either by molecular rotation on the cone or by rotation of the molecule about its long axis (so-called chirality flipping), or by both mechanisms simultaneously. When the smectic layers of the B₂ phase are non-deformed and parallel the rotation of molecules under an external electric field occurs readily on the surface of the cone, while rotation around the long molecular axis is hindered by an energy barrier. Imposed deformation of smectic layers leads to interaction between local layer curvatures and molecular orientation, which results in the energy barrier hindering the molecular rotation by a cone. For appropriate constants describing this interaction the energy barrier can be so high that chirality flipping becomes the principal switching mode. An increase in the electric field can eliminate layer curvature, and therefore the energy barrier, so that switching with molecular rotation on the cone becomes possible. In the present contribution these mechanisms of switching are discussed and the influence of layer curvature on the switching mode is demonstrated.     

On the solvation of the Zn2+ ion in methanol: a combined quantum mechanics, molecular dynamics, and EXAFS approach

The solvation properties of the Zn(2+) ion in methanol solution have been investigated using a combined approach based on molecular dynamics (MD) simulations and extended X-ray absorption fine structure (EXAFS) experimental results. The quantum mechanical potential energy surface for the interaction of the Zn(2+) ion with a methanol molecule has been calculated taking into account the effect of bulk solvent by the polarizable continuum model (PCM). The effective Zn-methanol interactions have been fitted by suitable analytical potentials, and have been utilized in the MD simulation to obtain the structural properties of the solution. The reliability of the whole procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The structural parameters of the first solvation shells issuing from the MD simulations provide an effective complement to the EXAFS experiments.     

Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets

The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium. Simple Lennard-Jones-like pair potentials, on the other hand, fall short in providing the required flexibility and accuracy in order to account for chemical reactions of the solute molecule. Here, a general scheme of constructing sufficiently accurate site-site potentials for use in typical quantum simulations is presented. This scheme employs atom-based grids, accounts for local and global minima, and is applied to the special case of a HCl(H(2)O)(4) cluster solvated by helium. As a first step, accurate interaction energies of a helium atom with a set of representative configurations sampled from a trajectory following the dissociation of the HCl(H(2)O)(4) cluster were computed using an efficient combination of density functional theory and symmetry-adapted perturbation theory, i.e. the DFT-SAPT approach. For each of the sampled cluster configurations, a helium atom was placed at several hundred positions distributed in space, leading to an overall number of about 400,000 such quantum chemical calculations. The resulting total interaction energies, decomposed into several energetic contributions, served to fit a site-site potential, where the sites are located at the atomic positions and, additionally, pseudo-sites are distributed along the lines joining pairs of atom sites within the molecular cluster. This approach ensures that this solute-helium potential is able to describe both undissociated molecular and dissociated (zwitter-) ionic configurations, as well as the interconnecting reaction pathway without re-adjusting partial charges or other parameters depending on the particular configuration. Test calculations of the larger HCl(H(2)O)(5) cluster interacting with helium demonstrate the transferability of the derived site-site potential. This specific potential can be readily used in quantum simulations of such HCl/water clusters in bulk helium or helium nanodroplets, whereas the underlying construction procedure can be generalized to other molecular solutes in other atomic solvents such as those encountered in rare gas matrix isolation spectroscopy.     

Kinetic Energy Partition Method for Competing Modes

We present a new basis set expansion method for quantum dynamics systems with two competing modes where the interaction potentials are equally dominant. The new idea introduced here is a kinetic energy partition scheme instead of the usual division of the potential energy. The partition results in two kinetic energy terms with their effective masses. By distributing each partial kinetic energy to the respective potential, the full Hamiltonian can be expressed as the sum of the two competing modes. The solution procedure is illustrated by using a system consisting of a particle under the action of two harmonic potentials with different equilibrium distances and force constants. Next we apply this method to obtain the potential energy curves for the prototype hydrogen molecule ion. This new expansion converges very fast to the exact solutions for both eigenvalues and eigenfunctions.     

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study

Using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, we address the relationship between molecular conformation and the biomedical function of arylamide polymers. Specifically, we have developed new torsional parameters for a class of these polymers and applied them in a study of the interaction between a representative arylamide and one of its biomedical targets, the anticoagulant drug heparin. Our main finding is that the torsional barrier of a C(aromatic)-C(carbonyl) bond increases significantly upon addition of an o-OCH2CH2NH3+ substituent on the benzene ring. Our molecular dynamics studies that are based on the original general AMBER force field (GAFF) and GAFF modified to include our newly developed torsional parameters show that the binding mechanism between the arylamide and heparin is very sensitive to the choice of torsional potentials. Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used.     

Intermolecular torsional motion of a π-aggregated dimer probed by two-dimensional electronic spectroscopy

The energetic splitting of the two exciton states of a molecular dimer depends strongly on the relative orientation of the monomers with respect to each other. The curvature of the corresponding adiabatic potential energy surfaces can lead to torsional motion of the monomers. It has been suggested recently that this torsional motion could provide a possible relaxation mechanism for the upper state which proceeds via a crossing of the two singly excited state potentials. Another, competing, relaxation mechanism is provided by coupling to the environment, leading to direct exciton relaxation. Here we examine theoretically the combined dynamics of torsional motion and excitonic relaxation for a π-aggregated dimer. Using two-dimensional (2D) spectroscopy, it is shown how torsional motion through a crossing of the adiabatic excitonic potential surfaces could be distinguished from direct relaxation. For the calculations a mixed quantum/classical approach is used, where the torsional motion is treated by an Ehrenfest type of equation, while the excitonic dynamics including dephasing and direct relaxation is described by a quantum master equation.     

An application of the novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: An ionic dissociation of a water molecule in the supercritical water

A novel quantum chemical approach recently developed has been applied to an ionic dissociation of a water molecule (2H(2)O-->H(3)O(+)+OH(-)) in ambient and supercritical water. The method is based on the quantum mechanical/molecular mechanical (QM/MM) simulations combined with the theory of energy representation (QM/MM-ER), where the energy distribution function of MM solvent molecules around a QM solute serves as a fundamental variable to determine the hydration free energy of the solute according to the rigorous framework of the theory of energy representation. The density dependence of the dissociation free energy in the supercritical water has been investigated for the density range from 0.1 to 0.6 g/cm(3) with the temperature fixed at a constant. It has been found that the product ionic species significantly stabilizes in the high density region as compared with the low density. Consequently, the dissociation free energy decreases monotonically as the density increases. The decomposition of the hydration free energy has revealed that the entropic term (-TDeltaS) strongly depends on the density of the solution and dominates the behavior of the dissociation free energy with respect to the variation of the density. The increase in the entropic term in the low density region can be attributed to the decrease in the translational degrees of freedom brought about by the aggregation of solvent water molecules around the ionic solute.     

Quantum study of peroxidic bonds and torsional levels for ROOR' molecules (R, R'=H, F, Cl, NO, CN)

We present here a systematic study by quantum mechanical methods of a series of molecules (HOOF, HOOCl, HOONO, HOOCN, FOOF, ClOOF, ClOOCl, and FOONO), corresponding to substitutions of one or both hydrogens in hydrogen peroxide. The emphasis is on the structural and energetic properties and on the features of the internal modes, in particular, the torsion around the O-O bond, which leads to the chirality changing isomerization. The cis and trans barriers appear to vary remarkably upon substitution by halogen groups. They are compared with experimental and theoretical information, when available, and analyzed by reference to a previous systematic analysis of the effects of alkyl substitutions. Torsional levels were calculated, and their distribution as a function of temperature was determined. This information is of interest for statistical approaches to equilibrium properties and to rates of processes where torsional anharmonicity is relevant, as required for recent atmospheric modeling studies and also for prototypical chiral separation experiments, in view of a possible dynamic mechanism for chirality exchange by molecular collisions. Dipole moments are also presented.     

Mixed quantum-classical dynamics in the adiabatic representation to simulate molecules driven by strong laser pulses

The dynamics of molecules under strong laser pulses is characterized by large Stark effects that modify and reshape the electronic potentials, known as laser-induced potentials (LIPs). If the time scale of the interaction is slow enough that the nuclear positions can adapt to these externally driven changes, the dynamics proceeds by adiabatic following, where the nuclei gain very little kinetic energy during the process. In this regime we show that the molecular dynamics can be simulated quite accurately by a semiclassical surface-hopping scheme formulated in the adiabatic representation. The nuclear motion is then influenced by the gradients of the laser-modified potentials, and nonadiabatic couplings are seen as transitions between the LIPs. As an example, we simulate the process of adiabatic passage by light induced potentials in Na(2) using the surface-hopping technique both in the diabatic representation based on molecular potentials and in the adiabatic representation based on LIPs, showing how the choice of the representation is crucial in reproducing the results obtained by exact quantum dynamical calculations.     

Multiscale modeling of materials based on force and charge density fidelity

The approximate representation of a quantum solid as an equivalent composite semiclassical solid is considered for insulating materials. The composite is comprised of point ions moving on a potential energy surface. In the classical bulk domain this potential energy is represented by potentials constructed to give the same structure and elastic properties as the underlying quantum solid. In a small local quantum domain the potential is determined from a detailed quantum calculation of the electronic structure. The new features of this well-studied problem are (1) a clearly stated theoretical context in which approximations leading to the model are introduced, (2) the representation of the classical domain by potentials focused on reproducing the specific quantum response being studied, (3) development of "pseudoatoms" for a realistic treatment of charge densities where bonds have been broken to define the environment of the quantum domain, and (4) inclusion of polarization effects on the quantum domain due to its distant bulk environment. This formal structure is illustrated in detail for a SiO(2) nanorod. More importantly, each component of the proposed modeling is tested quantitatively for this case, verifying its accuracy as a faithful multiscale model of the original quantum solid. To do so, the charge density of the entire nanorod is calculated quantum mechanically to provide the reference by which to judge the accuracy of the modeling. The construction of the classical potentials, the rod, the pseudoatoms, and the multipoles is discussed and tested in detail. It is then shown that the quantum rod, the rod constructed from the classical potentials, and the composite classical/quantum rod all have the same equilibrium structure and response to elastic strain. In more detail, the charge density and forces in the quantum subdomain are accurately reproduced by the proposed modeling of the environmental effects even for strains beyond the linear domain. The accuracy of the modeling is shown to apply for two quite different choices for the underlying quantum chemical method: transfer Hamiltonian and density functional methods.     

Quantum algorithm for obtaining the energy spectrum of molecular systems

Simulating a quantum system is more efficient on a quantum computer than on a classical computer. The time required for solving the Schr?dinger equation to obtain molecular energies has been demonstrated to scale polynomially with system size on a quantum computer, in contrast to the well-known result of exponential scaling on a classical computer. In this paper, we present a quantum algorithm to obtain the energy spectrum of molecular systems based on the multiconfigurational self-consistent field (MCSCF) wave function. By using a MCSCF wave function as the initial guess, the excited states are accessible. Entire potential energy surfaces of molecules can be studied more efficiently than if the simpler Hartree-Fock guess was employed. We show that a small increase of the MCSCF space can dramatically increase the success probability of the quantum algorithm, even in regions of the potential energy surface that are far from the equilibrium geometry. For the treatment of larger systems, a multi-reference configuration interaction approach is suggested. We demonstrate that such an algorithm can be used to obtain the energy spectrum of the water molecule.     

Force-field parametrization and molecular dynamics simulations of Congo red

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.     

A minimal model of potential energy surface for H2O?HCl

In this paper, we present a model of potential energy surface for the H₂O HCl system, consisting in the exact transformation of quantum chemical input data related to a minimal number of significant configurations. Both molecules are assumed as rigid. The interaction potential is given by an expansion in real spherical harmonics depending on the distance between the two centers of mass of the molecules and on four angles that define their mutual orientation. The main target of this work is the construction of a model of potential energy surface that requires a limited number of single energy points, which is suitable for applications to classical and quantum molecular dynamics simulations, permitting interpolation and further implementation of different sets of input data.