Modeling quantum dynamics of photodetachment from closed‐shell anions: Static versus fluctuating well‐depth models

The electronic states of halide ions are modeled by a one‐dimensional Hamiltonian with a potential V(x)=−V₀e. The two parameters V₀ and σ are fixed by requiring V(x) to reproduce the experimentally observed ground‐state ionization potentials of the halide ions concerned. The potentials so generated are shown to support only one bound state in each case. The time‐dependent Fourier grid Hamiltonian method is used to follow the ionization dynamics in monochromatic light of fairly high intensities. The total Hamiltonian, in the most general case, reads H(t)=P/2m−V₀e−ϵ₀s(t)ex sin(ωt). For pulsed fields [s(t)=sin²(πt/t_p)], the computed ionization rate constants are seen to increase with increase in the peak intensity (ϵ₀) of the electric field of light. The possibility of additional transient bound states being generated at the high intensities of light and its possible consequences on the observed ionization rates are explored. The environmental effects on the dynamics are sought to be modeled by allowing the well depth (V₀) to fluctuate randomly [V₀(t)=V₀+ΔVR(t); R(t) randomly fluctuates between +1 and −1 with time, ΔV is fixed]. The ionization rate constants (k_ϵ) are shown to be significantly affected by fluctuations in V₀ and pass through a well‐defined minimum in each case for a certain specified frequency of fluctuation. An alternative model potential V(x)=−V₀e^−σx is also shown to yield similar results. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 469–478, 1999     

Photodetachment dynamics from closed‐shell anions in the presence of a bichromatic field

I have studied the dynamics of photodetachment from closed‐shell anions in the presence of a two‐color (bichromatic) laser field. The electronic states of halide ions are modeled by a 1‐D Hamiltonian with a potential V(x) = ?V₀e. The two parameters V₀ and σ are fixed by requiring V(x) to reproduce the experimentally observed ground‐state ionization energy of the halide ions concerned. The potentials so generated are shown to support only one bound state in each case. The time‐dependent Fourier grid Hamiltonian method is used to follow the detachment dynamics with fairly high intensities of light. The environmental effects on the dynamics are sought to be modeled by allowing the well depth (V₀) to fluctuate randomly (V₀(t) = V₀[1 + ΔVR(t)]; R(t) randomly fluctuates between +1 and ?1 with time, when ΔV is fixed). The average detachment rate constants k_av are seen to increase with increase in the intensities of used bichromatic field. An alternative model potential, V(x) = ?V₀e^?σx, is also shown to yield similar results. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Tunneling dynamics of a double‐well oscillator: Effects of barrier fluctuation and thermal modulation

The tunneling dynamics of a particle moving in a bistable potential with fluctuating barrier is studied. For barriers fluctuating randomly in time we show by exact numerical calculation the significant effect of barrier fluctuation on the tunneling behavior of the particle. At nonzero temperatures the computed tunneling rate constant passes through a maximum when plotted against fluctuation frequency. The resonant frequency (at which the maximum appears) slowly decreases with increase in temperature and attains a constant value at higher temperature and it increases linearly with increase in barrier height of the potential. Another important observation is that in presence of barrier fluctuation the dependence of tunneling rate constant on temperature is strongly guided by the barrier fluctuation frequency. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 280–285, 2003     

Chemiluminescence of 1,2‐dioxetanone studied by a closed‐shell DFT approach

The chemiluminescence of simple 1,2‐dioxetanone has already been studied by both multiconfigurational and density functional theory calculations. The former approach revealed a step‐wise biradical mechanism for its decomposition, whereas the latter revealed a concerted mechanism. The first approach was not in line with both computational and experimental findings, whereas the second mechanism was. Due to these apparent mechanistic contradictions and some concerns regarding our concerted mechanism, and the use of a closed‐shell approach and different methods for geometry and single‐point calculations, we have revisited the chemiluminescence of this molecule. Once again the concerted mechanism was found to be prevailing, and a closed‐shell approach was able to rationalize the chemiluminescence of 1,2‐dioxetanone. It was once again noted that an open‐shell and a step‐wise biradical mechanism cannot explain the chemiluminescence of this molecule. © 2013 Wiley Periodicals, Inc.     

Quantum dynamics of relaxation of a pair of coupled Morse oscillators: Effects of mass and electrical asymmetries

A multiconfiguration time‐dependent Hartree method based recipe is used to study the role of mass and electrical asymmetry in controlling the quantum dynamics of relaxation of a locally excited O? H bond in a water molecule, modeled by a pair of interacting Morse oscillators. The fast periodic energy transfer between the two equivalent O? H bonds in H? O? H is replaced by a rather slow process when one of the H atom is replaced by a deuterium atom. Application of static electric field along the O? D bond in HOD molecule is seen to either enhance or damp the relaxation rate, depending on the strength of the applied field. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Atomistic detailed free‐energy landscape of intrinsically disordered protein studied by multi‐scale divide‐and‐conquer molecular dynamics simulation

Calcineurin (CaN) is a eukaryotic serine/threonine protein phosphatase activated by both Ca²⁺ and calmodulin (CaM), including intrinsically disordered region (IDR). The region undergoes folding into an α‐helix form in the presence Ca²⁺‐loaded CaM. To sample the ordered structure of the IDR by conventional all atom model (AAM) molecular dynamics (MD) simulation, the IDR and Ca²⁺‐loaded CaM must be simultaneously treated. However, it is time‐consuming task because the coupled folding and binding should include repeated binding and dissociation. Then, in this study, we propose novel multi‐scale divide‐and‐conquer MD (MSDC‐MD), which combines AAM‐MD and coarse‐grained model MD (CGM‐MD). To speed up the conformation sampling, MSDC‐MD simulation first treats the IDR by CGM to sample conformations from wide conformation space; then, multiple AAM‐MD in a limited area is initiated using the resultant CGM conformation, which is reconstructed by homology modeling method. To investigate performance, we sampled the ordered conformation of the IDR using MSDC‐MD; the root‐mean‐square distance (RMSD) with respect to the experimental structure was 2.23 Å.     

Development of spin‐dependent relativistic open‐shell Hartree–Fock theory with time‐reversal symmetry (II): The restricted open‐shell approach

An open‐shell Hartree–Fock (HF) theory for spin‐dependent two‐component relativistic calculations, termed the Kramers‐restricted open‐shell HF (KROHF) method, is developed. The present KROHF method is defined as a relativistic analogue of ROHF using time‐reversal symmetry and quaternion algebra, based on the Kramers‐unrestricted HF (KUHF) theory reported in our previous study (Int. J. Quantum Chem., doi: 10.1002/qua.25356 ). As seen in the nonrelativistic ROHF theory, the ambiguity of the KROHF Fock operator gives physically meaningless spinor energies. To avoid this problem, the canonical parametrization of KROHF to satisfy Koopmans' theorem is also discussed based on the procedure proposed by Plakhutin et al. (J. Chem. Phys. 2006 , 125, 204110). Numerical assessments confirmed that KROHF using Plakhutin's canonicalization procedure correctly gives physical spinor energies within the frozen‐orbital approximation under spin–orbit interactions.     

Possible mechanism of BN fullerene formation from a boron cluster: Density‐functional tight‐binding molecular dynamics simulations

We simulate the formation of a BN fullerene from an amorphous B cluster at 2000 K by quantum mechanical molecular dynamics based on the density‐functional tight‐binding method. We run 30 trajectories 200 ps in length, where N atoms are supplied around the target cluster, which is initially an amorphous B₃₆ cluster. Most of the incident N atoms are promptly incorporated into the target cluster to form B‐N‐B bridges or NB₃ pyramidal local substructures. BN fullerene formation is initiated by alternating BN ring condensation. Spontaneous atomic rearrangement and N₂ dissociation lead to the construction of an sp² single‐shelled structure, during which the BN cluster undergoes a transition from a liquid‐like to a solid‐like state. Continual atomic rearrangement and sporadic N₂ dissociation decrease the number of defective rings in the BN cluster and increase the number of six‐membered rings, forming a more regular shell structure. The number of four‐membered rings tends to remain constant, and contributes to more ordered isolated‐tetragon‐rule ring placement. © 2016 Wiley Periodicals, Inc.     

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide‐and‐conquer,density‐functional tight‐binding,and massively parallel computation

The linear‐scaling divide‐and‐conquer (DC) quantum chemical methodology is applied to the density‐functional tight‐binding (DFTB) theory to develop a massively parallel program that achieves on‐the‐fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC‐DFTB potential energy surface are implemented to the program called DC‐DFTB‐K. A novel interpolation‐based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC‐DFTB‐K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC‐DFTB‐K program, a single‐point energy gradient calculation of a one‐million‐atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc.     

Electrohydrodynamics of spherical polyampholyte‐grafted nanoparticles: Multiscale simulations by coupling of molecular dynamics and lattice‐boltzmann method

We perform multiscale simulations based on the coupling of molecular dynamics and lattice‐Boltzmann (LB) method to study the electrohydrodynamics of a polyampholyte‐grafted spherical nanoparticle. The long‐range hydrodynamic interactions are modeled by coupling the movement of particles to a LB fluid. Our results indicate that the net‐neutral soft particle moves with a nonzero mobility under applied electric fields. We systematically explore the effects of different parameters, including the chain length, grafting density, electric field, and charge sequence, on the structures of the polymer layer and the electrophoretic mobility of the soft particle. It shows that the mobility of nanoparticles has remarkable dependence on these parameters. We find that the deformation of the polyampholyte chains and the ion distribution play dominant roles in modulating the electrokinetic behavior of the polyampholyte‐grafted particle. The enhancement or reduction in the accumulation of counterions around monomers can be attributed to the polymer layer structure and the conformational transition of the chains in the electric field. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1435–1447     

Development of spin‐dependent relativistic open‐shell Hartree–Fock theory with time‐reversal symmetry (I): The unrestricted approach

An open‐shell Hartree–Fock (HF) theory for spin‐dependent, two‐component relativistic calculations, termed the Kramers‐unrestricted HF (KUHF) method, is developed. The present KUHF method, which is formulated as a relativistic counterpart of nonrelativistic UHF, is based on quaternion algebra and partly uses time‐reversal symmetry. The fundamental characteristics of KUHF are discussed in this study. From numerical assessments, it was revealed that KUHF gives a corresponding solution to nonrelativistic UHF; furthermore, KUHF properly describes spin‐orbit interactions. In addition, KUHF can improve the self‐consistent field convergence behavior in spin‐dependent calculations, for example, for f‐block elements.     

Influence of variation of a side chain on the folding equilibrium of a β‐peptide: Limitations of one‐step perturbation

In a recent study (Lin et al., Helv. Chim. Acta 2011, 94 , 597), the one‐step perturbation method was applied to tackle a challenging computational problem, that is, the calculation of the folding free enthalpies ΔG_F,U of six hepta‐β‐peptides with different, Ala, Val, Leu, Ile, Ser, or Thr, side chains in the fifth residue. The ΔG_F,U values obtained using one‐step perturbation based on a single molecular dynamics simulation of a judiciously chosen reference state with soft‐core atoms in the side chain of the fifth residue showed an overall accuracy of about k_BT for the four peptides with nonpolar side chains, but twice as large deviations were observed for the peptides with polar side chains. Here, alternative reference‐state Hamiltonians that better cover the conformational space relevant to these peptides are investigated, and post simulation rotational sampling of the χ₁ and χ₂ torsional angles of the fifth residue is carried out to sample different orientations of the side chain. A reference state with rather soft atoms yields accurate ΔG_F,U values for the peptides with the Ser and Thr side chains, but it failed to correctly predict the folding free enthalpy for one peptide with a nonpolar side chain, that is, Leu. Based on the results and those of earlier studies, possible ways to improve the accuracy of the efficient one‐step perturbation technique to compute free enthalpies of folding are discussed. © 2013 Wiley Periodicals, Inc.     

Apparent relaxation‐time spectrum cutoff in dilute polymer solutions: An effect of solvent dynamics

The apparent short time cutoff of the relaxation‐time spectrum at surprisingly long times for polymers in solution is a well known but not yet understood observation. To elucidate its origins we revisit viscoelastic and oscillatory flow birefringence data for solutions and melts of two linear polymers (polystyrene and polyisoprene) and present new measurements of oscillatory flow birefringence of the latter. Previous measurements have suggested that the “flexibility” of both polymers in solution is smaller than in the melt on the basis of the breadth of the relaxation‐time spectrum of the solution as compared with that of the melt. Our new measurements have explored a higher effective frequency range than was previously possible. This has allowed us to observe the effect of the rotational relaxation time of the solvent on the dynamics of the solution at high frequencies. To obtain the polymer global motion contribution, one now needs to subtract from the solution properties a frequency‐dependent complex solvating environment contribution. We show that the decrease in apparent “flexibility” for solutions arises from the presence of a solvent that exhibits a rotational relaxation time and thus simple viscoelastic behavior somewhat near the frequency window of the experiment. Although recent predictions of a model for a chain in a solvent with a single relaxation time are in qualitative agreement with our results, our data suggest that the solution results may reflect the influence of solvent on the development of the “entropic spring” forces at short times. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2860–2873, 2001     

Energy transfer dynamics and kinetics of elementary processes (promoted) by gas‐phase CO2‐N2 collisions: Selectivity control by the anisotropy of the interaction

In this work, we exploit a new formulation of the potential energy and of the related computational procedures, which embodies the coupling between the intra and intermolecular components, to characterize possible propensities of the collision dynamics in energy transfer processes of interest for simulation and control of phenomena occurring in a variety of equilibrium and nonequilibrium environments. The investigation reported in the paper focuses on the prototype CO₂–N₂ system, whose intramolecular component of the interaction is modeled in terms of a many body expansion while the intermolecular component is modeled in terms of a recently developed bonds‐as‐interacting‐molecular‐centers' approach. The main advantage of this formulation of the potential energy surface is that of being (a) truly full dimensional (i.e., all the variations of the coordinates associated with the molecular vibrations and rotations on the geometrical and electronic structure of the monomers, are explicitly taken into account without freezing any bonds or angles), (b) more flexible than other usual formulations of the interaction and (c) well suited for fitting procedures better adhering to accurate ab initio data and sensitive to experimental arrangement dependent information. Specific attention has been given to the fact that a variation of vibrational and rotational energy has a higher (both qualitative and quantitative) impact on the energy transfer when a more accurate formulation of the intermolecular interaction (with respect to that obtained when using rigid monomers) is adopted. This makes the potential energy surface better suited for the kinetic modeling of gaseous mixtures in plasma, combustion and atmospheric chemistry computational applications. © 2016 Wiley Periodicals, Inc.     

Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose‐1,6‐bisphosphatase inhibitors

In an attempt to establish the criteria for the length of simulation to achieve the desired convergence of free energy calculations, two studies were carried out on chosen complexes of FBPase‐AMP mimics. Calculations were performed for varied length of simulations and for different starting configurations using both conventional‐ and QM/MM‐FEP methods. The results demonstrate that for small perturbations, 1248 ps simulation time could be regarded a reasonable yardstick to achieve convergence of the results. As the simulation time is extended, the errors associated with free energy calculations also gradually tapers off. Moreover, when starting the simulation from different initial configurations of the systems, the results are not changed significantly, when performed for 1248 ps. This study carried on FBPase‐AMP mimics corroborates well with our previous successful demonstration of requirement of simulation time for solvation studies, both by conventional and ab initio FEP. The establishment of aforementioned criteria of simulation length serves a useful benchmark in drug design efforts using FEP methodologies, to draw a meaningful and unequivocal conclusion. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence

Ultrafast excited‐state deactivation dynamics of small cytosine (Cy) and 1‐methylcytosine (1mCy) microhydrates, Cy?(H₂O)_1‐3 and 1mCy?(H₂O)_1,2, produced in a supersonic expansion have been studied by mass‐selected femtosecond pump–probe photoionization spectroscopy at about 267 nm excitation. The seeded supersonic expansion of Ar/H₂O gas mixtures allowed an extensive structural relaxation of Cy and 1mCy microhydrates to low‐energy isomers. With the aid of electronic structure calculations, we assigned the observed ultrafast dynamics to the dominant microhydrate isomers of the amino‐keto tautomer of Cy and 1mCy. Excited‐state lifetimes of Cy?(H₂O)_1‐3 measured here are 0.2–0.5 ps. Comparisons of the Cy?H₂O and 1mCy?H₂O transients suggest that monohydration at the amino Watson–Crick site induces a substantially stronger effect than at the sugar‐edge site in accelerating excited‐state deactivation of Cy.