Two‐dimensional reactive scattering with transmitted quantum trajectories

A simple and easy‐to‐implement method is presented for the study of time‐dependent reaction dynamics by propagating an ensemble of transmitted quantum trajectories. During the trajectory evolution, reflected trajectories are gradually removed and all the remaining trajectories represent the transmitted subensemble. The removal process of reflected trajectories avoids numerical instabilities arising from node formation in the reactant region, and allows stable long‐time propagation of transmitted trajectories. This method is applied to a two‐dimensional model chemical reaction. Excellent computational results are obtained for the time‐dependent reaction probabilities evaluated by the time integration of the probability flux. © 2014 Wiley Periodicals, Inc.     

Reconstructing interference fringes in slit experiments by complex quantum trajectories

There are external and internal representations for a quantum state Ψ. External representation is commonly adopted in the standard quantum mechanics by exploiting probability density function Ψ*Ψ to explain the observed interference fringes in slit experiments. On the other hand, in quantum Hamilton mechanics, the quantum state Ψ has a dynamical representation that reveals the internal mechanism underlying the externally observed interference fringes. The internal representation of Ψ is described by a set of Hamilton equations of motion, by which quantum trajectories of a particle moving in Ψ can be solved. In this article, millions of complex quantum trajectory connecting slits to a screen are solved from the Hamilton equations, and the statistical distribution of their arrivals on the screen is shown to reproduce the observed interference fringes. This appears to be the first quantitative verification of the equivalence between the trajectory‐based statistics and the wavefunction‐based statistics on slit experiments. © 2012 Wiley Periodicals, Inc.     

Electronic quantum trajectories in a quantum dot

This article gives a quantum‐trajectory demonstration of the observed electric, magnetic, and thermal effects on a quantum dot with circular or elliptic shape. By applying quantum trajectory method to a quantum dot, we reveal the quantum‐mechanical meanings of the classical concepts of backscattering and commensurability, which were used in the literature to explain the peak locations of the magnetoresistance curve. Under the quantum commensurability condition, electronic quantum trajectories in a circular quantum dot are shown to be stationary like a standing wave, whose presence increases the electrical resistance. A hidden quantum effect called magnetic stagnation is discovered and shown to be the main cause of the observed jumps of the magnetoresistance curve. Quantum trajectories in an elliptic quantum dot are found to be chaotic and an index of chaos called Lyapunov exponent is proposed to measure the irregularity of the various quantum trajectories. It is shown that the response of the Lyapunov exponent to the applied magnetic field captures the main features of the experimental magnetoresistance curve. © 2014 Wiley Periodicals, Inc.     

Simple methods for the optimization of complex‐valued kurtosis as a projection index

With the advancement of modern techniques, complex‐valued data have become more important in chemistry and many other areas. The data collected are often multi‐dimensional. This imposes an increasing demand on the tools used for the analysis of complex‐valued data. In multivariate data analysis, projection pursuit is a useful and important technique that in many cases gives better results than principal component analysis. One important projection pursuit variant uses the real‐valued kurtosis as its projection index and has been shown to be a powerful approach to address different problems. However, using the complex‐valued kurtosis as a projection index to deal with complex‐valued data is rare. This is, to a great extent, due to the lack of simple and fast optimization algorithms. In this work, simple and rapidly executed optimization algorithms for the complex‐valued kurtosis used as a projection index are proposed. The developed algorithms have a variety of advantages: no requirement for sphering or strong‐uncorrelation transformation of the data in advance, no assumption for the latent components (source signals) to be circular or non‐circular, search for maxima or minima on users' requirements, and users having the option to choose uncorrelated scores or orthogonal projection vectors. The mathematical development of the algorithms is described and simulated and real experimental data are employed to demonstrate the utility of the proposed algorithms. Copyright © 2015 John Wiley & Sons, Ltd.     

Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.     

Quantum tunneling in a periodically driven double well system: Entangled trajectory molecular dynamics method

We study a wavepacket tunneling in one‐dimensional periodically driven double‐well system using entangled trajectory molecular dynamics method. The tunneling dynamics dependents on the amplitude and frequency of the driven force are present. Both resonant and nonresonant tunneling process are enhanced by the driven force when the system is chaotic under classical dynamics. We give entangled trajectory in phase space compared to corresponding classical trajectory with same initial state to visually show quantum tunneling process. The average values of quantum tunneling probability after long time evolution have been shown in the parameter spaces, the effect of resonance and chaos on the tunneling dynamics are present. The relation between chaos and the uncertainly product is discussed in the end. © 2016 Wiley Periodicals, Inc.     

Calculation of wave‐functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation

The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009 , 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self‐consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree–Fock–Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self‐consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave‐function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem. © 2013 Wiley Periodicals, Inc.     

Solution of the “Classical” Schrödinger equation for a driven symmetric triple well: A comparison with its classical counterpart

The behavior of a driven symmetric triple well potential has been studied by developing an algorithm where the well‐established Bohmian mechanics and time‐dependent Fourier Grid Hamiltonian method are incorporated and the quantum theory of motion (QTM) phase space structures of the particle are constructed, both in “nonclassical” and “classical” limits. Comparison of QTM phase space structures with their classical analogues shows both similarity as well as dissimilarities. The temporal nature and the spatial symmetry of applied perturbation play crucial roles in having similar phase space structures. © 2016 Wiley Periodicals, Inc.     

Real‐time quantum chemistry

Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be able to treat ever larger molecules or molecular assemblies—especially linear and sublinear scaling techniques are devoted to the accomplishment of this goal. However, as many chemical reactions are rather local, they usually involve only a limited number of atoms so that models of about 200 (or even less) atoms embedded in a suitable environment are sufficient to study their mechanisms. Thus, the system size does not need to be enlarged, but remains constant for reactions of this type that can be described by less than 200 atoms. The question then arises how fast one can obtain the quantum chemical results. This question is not directly answered by linear‐scaling techniques. In fact, ideas such as haptic quantum chemistry (HQC) or interactive quantum chemistry require an immediate provision of quantum chemical information which demands the calculation of data in “real time.” In this perspective, we aim at a definition of real‐time quantum chemistry, explore its realm and eventually discuss applications in the field of HQC. For the latter, we elaborate whether a direct approach is possible by virtue of real‐time quantum chemistry. © 2012 Wiley Periodicals, Inc.     

Sequence‐Dependent Duplex Stabilization upon Formation of a Metal‐Mediated Base Pair

An artificial nucleoside surrogate with 1H‐imidazo[4,5‐f][1,10]phenanthroline ( P ) acting as an aglycone has been introduced into DNA oligonucleotide duplexes. This nucleoside surrogate can act as a bidentate ligand, and so is useful in the context of metal‐mediated base pairs. Several duplexes involving a hetero base pair with an imidazole nucleoside have been investigated. The stability of DNA duplexes incorporating the respective Ag^I‐mediated base pairs strongly depends on the sequence context. Quantum mechanical/molecular mechanical (QM/MM) calculations have been performed in order to gain insight into the factors determining this sequence dependence. The results indicated that, in addition to the stabilizing effect that results from the formation of coordinative bonds, destabilizing effects may occur when the artificial base pair does not fit optimally into the surrounding B‐DNA duplex.     

Fragment‐based quantum mechanical calculation of protein–protein binding affinities

The electrostatically embedded generalized molecular fractionation with conjugate caps (EE‐GMFCC) method has been successfully utilized for efficient linear‐scaling quantum mechanical (QM) calculation of protein energies. In this work, we applied the EE‐GMFCC method for calculation of binding affinity of Endonuclease colicin–immunity protein complex. The binding free energy changes between the wild‐type and mutants of the complex calculated by EE‐GMFCC are in good agreement with experimental results. The correlation coefficient (R) between the predicted binding energy changes and experimental values is 0.906 at the B3LYP/6‐31G*‐D level, based on the snapshot whose binding affinity is closest to the average result from the molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) calculation. The inclusion of the QM effects is important for accurate prediction of protein–protein binding affinities. Moreover, the self‐consistent calculation of PB solvation energy is required for accurate calculations of protein–protein binding free energies. This study demonstrates that the EE‐GMFCC method is capable of providing reliable prediction of relative binding affinities for protein–protein complexes. © 2018 Wiley Periodicals, Inc.     

A study of entangled systems in the many‐body signed particle formulation of quantum mechanics

Recently a new formulation of quantum mechanics has been introduced, based on signed classical field‐less particles interacting with an external field by means of only creation and annihilation events. In this article, we extend this novel theory to the case of many‐body problems. We show that, when restricted to spatial finite domains and discrete momentum space, the proposed extended theory is equivalent to the time‐dependent many‐body Wigner Monte Carlo method. In this new picture, the treatment of entangled systems comes naturally and, therefore, we apply it to the study of quantum entangled systems. The latter is represented in terms of two Gaussian wave packets moving in opposite directions. We introduce the presence of a dissipative background and show how the entanglement is affected by different (controlled) configurations.     

Stochastic search for isomers on a quantum mechanical surface

In studying molecules with unusual bonding and structures, it is desirable to be able to find all the isomers that are minima on the energy surface. A stochastic search procedure is described for seeking all the isomers on a surface defined by quantum mechanical calculations involving random kicks followed by optimization. It has been applied to searching for singlet structures for C6 using the restricted Hartree-Fock/6-311G basis set. In addition to the linear chain and ring previously investigated, 11 additional structures (A-K) were located at this level. These provide a basis for discussing qualitative bonding motifs for this carbon cluster. The application of a similar idea to searching for transition states is discussed.     

A method to calculate the one‐electron reduction potentials for nitroaromatic compounds based on gas‐phase quantum mechanics

Nitroaromatic compounds (NACs) are widespread environmental contaminants, and the one‐electron reduction potential (E) is an important parameter used in modeling their environmental fate. We have identified a method that is both accurate and efficient to predict E values for NACs, using gas‐phase quantum mechanics (QM) calculations combined with empirical correlations. First, the adiabatic electron affinity (EA) at 0 K is calculated using the B98/MG3S method, and the predictions are scaled by a factor of 0.802 to account for systematic errors in the density functional calculations. Second, the E values are predicted from a linear correlation between E and EA. Using this method, E values were predicted with a mean absolute deviation from measured values of 0.021 V for the 14 NACs used to obtain the correlation and 0.029 V for six additional NACs. This represents a substantial improvement in accuracy over predictions by other QM methods, which are affected by large errors in solvation or aqueous‐phase calculations for some compounds. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010.     

Mechanism of proteolysis in matrix metalloproteinase‐2 revealed by QM/MM modeling

The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase‐2 (MMP‐2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all‐atom three‐dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace‐Gln‐Gly～Ile‐Ala‐Gly‐Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four‐step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C? N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5–10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate‐limiting step in MMP‐2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations. © 2015 Wiley Periodicals, Inc.     

Interaction of a finite quantum system with an infinite quantum system that contains a single one-parameter eigenvalue band

Interaction of a finite quantum system that contains ρ eigenvalues and eigenstates with an infinite quantum system that contains a single one-parameter eigenvalue band is considered. A new approach for the treatment of the combined system is developed. This system contains embedded eigenstates with continuous eigenvalues , and, in addition, it may contain isolated eigenstates with discrete eigenvalues . Two ρ × ρ eigenvalue equations, a generic eigenvalue equation and a fractional shift eigenvalue equation are derived. It is shown that all properties of the system that interacts with the system can be expressed in terms of the solutions to those two equations. The suggested method produces correct results, however strong the interaction between quantum systems and . In the case of the weak interaction this method reproduces results that are usually obtained within the formalism of the perturbation expansion approach. However, if the interaction is strong one may encounter new phenomena with much more complex behavior. This is also the region where standard perturbation expansion fails. The method is illustrated with an example of a two-dimensional system that interacts with the infinite system that contains a single one-parameter eigenvalue band. It is shown that all relevant completeness relations are satisfied, however strong the interaction between those two systems. This provides a strong verification of the suggested method.     

Glucose transformation to 5‐hydroxymethylfurfural in acidic ionic liquid: A quantum mechanical study

Isomerization and transformation of glucose and fructose to 5‐hydroxymethylfurfural (HMF) in both ionic liquids (ILs) and water has been studied by the reference interaction site model self‐consistent field spatial electron density distribution (RISM‐SCF‐SEDD) method coupled with ab initio electronic structure theory, namely coupled cluster single, double, and perturbative triple excitation (CCSD(T)). Glucose isomerization to fructose has been investigated via cyclic and open chain mechanisms. In water, the calculations support the cyclic mechanism of glucose isomerization; with the predicted activation free energy is 23.8 kcal mol^?1 at experimental condition. Conversely, open ring mechanism is more favorable in ILs with the energy barrier is 32.4 kcal mol^?1. Moreover, the transformation of fructose into HMF via cyclic mechanism is reasonable; the calculated activation barriers are 16.0 and 21.5 kcal mol^?1 in aqueous and ILs solutions, respectively. The solvent effects of ILs could be explained by the decomposition of free energies and radial distribution functions of solute‐solvent that are produced by RISM‐SCF‐SEDD. © 2015 Wiley Periodicals, Inc.