Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

Activation free energy for proton transfer in solution

Path integral molecular dynamics methods are employed to compute the free energy for proton transfer reactions for strongly hydrogen bonded systems in a polar solvent. The free energy profile is calculated using several different techniques, including: integration of the mean force acting on the proton path with its centroid constrained at different values, the integral form of the free energy calculation in the constrained-reaction-coordinate-dynamics ensemble and direct simulation of the unconstrained dynamics. The results show that estimates of the free energy barrier obtained by harmonic extrapolation are likely to be in error. Both quantum and classical results for the free energy are obtained and compared with simulations using adiabatic quantum dynamics. Comparison of the quantum and classical results show that there are quantum corrections to the solvent contributions to the free energy.     

Quantum dynamics of the CH3 fragment: a curvilinear coordinate system and kinetic energy operators

A curvilinear coordinate system for AB(3) fragments is given. The corresponding exact kinetic energy operator is derived and a series of simpler, progressively more approximate kinetic energy operators are suggested. The operators are tailored for quantum dynamics simulations using the multiconfigurational time-dependent Hartree approach. It is outlined how these fragment coordinates can be utilized to set up coordinate systems for larger systems such as AB(3)C or AB(3)CD. Calculations of the vibrational levels of CH(3) and quantum dynamics studies investigate the accuracy of the different kinetic energy operators suggested.     

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.     

Quantum dot-based energy transfer: perspectives and potential for applications in photodynamic therapy

Quantum dots have emerged as an important class of material that offers great promise to a diverse range of applications ranging from energy conversion to biomedicine. Here, we review the potential of using quantum dots and quantum dot conjugates as sensitizers for photodynamic therapy (PDT). The photophysics of singlet oxygen generation in relation to quantum dot-based energy transfer is discussed and the possibility of using quantum dots as photosensitizer in PDT is assessed, including their current limitations to applications in biological systems. The biggest advantage of quantum dots over molecular photosensitizers that comes into perspective is their tunable optical properties and surface chemistries. Recent developments in the preparation and photophysical characterization of quantum dot energy transfer processes are also presented in this review, to provide insights on the future direction of quantum dot-based photosensitization studies from the viewpoint of our ongoing research.     

多原子反应体系的高精度拟合势能面

本文介绍了近几年来我们组构建多原子反应体系的高精度拟合势能面的进展。我们基于神经网络(NN)方法,成功构建了多原子气相分子体系和气相分子在金属表面解离的一系列势能面。这些势能面的拟合精度相当高,并且经过了严格的量子动力学测试,能广泛应用到动力学研究中。我们还提出了一种新的置换不变势能面的拟合方法,即基本不变量神经网络方法(FI-NN)。基本不变量的使用极大地减少了神经网络输入层多项式的个数,有效提高了势能面的计算速度。     

Simulating quantum dynamics in classical environments

Methods for simulating the dynamics of composite systems, where part of the system is treated quantum mechanically and its environment is treated classically, are discussed. Such quantum–classical systems arise in many physical contexts where certain degrees of freedom have an essential quantum character while the other degrees of freedom to which they are coupled may be treated classically to a good approximation. The dynamics of these composite systems are governed by a quantum–classical Liouville equation for either the density matrix or the dynamical variables which are operators in the Hilbert space of the quantum subsystem and functions of the classical phase space variables of the classical environment. Solutions of the evolution equations may be formulated in terms of surface-hopping dynamics involving ensembles of trajectory segments interspersed with quantum transitions. The surface-hopping schemes incorporate quantum coherence and account for energy exchanges between the quantum and classical degrees of freedom. Various simulation algorithms are discussed and illustrated with calculations on simple spin-boson models but the methods described here are applicable to realistic many-body environments.     

Non-adiabatic molecular dynamics with quantum solvent effects

Three novel approaches extending quantum-classical non-adiabatic (NA) molecular dynamics (MD) to include quantum effects of solvent environments are described. In a standard NA-MD the solute subsystem is treated quantum mechanically, while the larger solvent part of a system is treated classically. The three novel approaches presented here are based on the Bohmian formulation of quantum mechanics, the stochastic Schrödinger equation for the evolution of open quantum systems and the quantized Hamilton dynamics generalization of classical mechanics. The approaches extend the standard NA-MD to incorporate the following quantum effects of the solvent. (1) Branching, i.e. the ability of solvent quantum wave packets to split and follow asymptotically diverging trajectories correlated with different quantum states of the solute. (2) Decoherence, i.e. loss of quantum interference within the solute subsystem induced by the diverging solvent trajectories. (3) Zero point energy that contributes to NA coupling and must be preserved during the energy exchange between solvent and solute degrees of freedom. The Bohmian quantum-classical mechanics, stochastic mean-field and quantized mean-field approximations incorporate the quantum solvent effects into the standard quantum-classical NA-MD in a straightforward and efficient way that can be easily applied to quantum dynamics of condensed phase chemical systems.     

Searching the Chemical Space of Bicyclic Dienes for Molecular Solar Thermal Energy Storage Candidates

Photoswitches are molecular systems that are chemically transformed subsequent to interaction with light and they find potential application in many new technologies. The design and discovery of photoswitch candidates require intricate molecular engineering of a range of properties to optimize a candidate to a specific applications, a task which can be tackled efficiently using quantum chemical screening procedures. In this paper, we perform a large scale screening of approximately half a million bicyclic diene photoswitches in the context of molecular solar thermal energy storage using ab initio quantum chemical methods. We further device an efficient strategy for scoring the systems based on their predicted solar energy conversion efficiency and elucidate potential pitfalls of this approach. Our search through the chemical space of bicyclic dienes reveals systems with unprecedented solar energy conversion efficiencies and storage densities that show promising design guidelines for next generation molecular solar thermal energy storage systems.     

A modified Ehrenfest method that achieves Boltzmann quantum state populations

A modification of the hybrid quantum/classical mean-field or Ehrenfest method is proposed which allows us to reproduce the Boltzmann quantum state populations when simulating the vibrational energy transfer between quantum systems and classical thermal baths. The modified Ehrenfest results are shown to be able to simulate the energy fluxes between the solute vibration and the classical solvent in the proper directions, depending on their relative temperatures.     

A multilayer multiconfigurational time-dependent Hartree approach for quantum dynamics on general potential energy surfaces

The multiconfigurational time-dependent Hartree (MCTDH) approach facilitates multidimensional quantum dynamics calculations by representing the wavepacket in an optimal set of time-dependent basis functions, called single-particle functions. Choosing these single-particle functions to be themselves multidimensional wavefunctions which are represented using a MCTDH representation, a multilayer MCTDH scheme has been constructed and used for quantum dynamics calculations treating up to 1000 degrees of freedom rigorously [Wang and Thoss, J. Chem. Phys. 199, 1289 (2003)]. The present work gives a practical scheme which facilitates the application of the multilayer MCTDH approach, which previously has only been employed to study systems described by model-type Hamiltonians, to molecular systems described by more complicated Hamiltonians and general potential energy surfaces. A multilayer extension of the correlation discrete variable representation (CDVR) scheme employed in MCTDH calculations studying quantum dynamics on general potential energy surfaces is developed and tested in a simple numerical application. The resulting multilayer MCTDH/CDVR approach might offer a perspective to rigorously describe the quantum dynamics of larger polyatomic systems.     

Calculation of the moscovium ground-state energy by quantum algorithms

We investigate the possibility to calculate the ground-state energy of the atomic systems on a quantum computer. For this purpose we evaluate the lowest binding energy of the moscovium atom with the use of the iterative phase estimation and variational quantum eigensolver (VQE). The calculations by the VQE are performed with a disentangled unitary coupled cluster ansatz and with various types of hardware-efficient ansatze. The optimization is performed with the use of the Adam and quantum natural gradients procedures. The scalability of the ansatze and optimizers is tested by increasing the size of the basis set and the number of active electrons. The number of gates required for the iterative phase estimation and VQE is also estimated.     

Long‐Distance Electronic Energy Transfer in Light‐Harvesting Supramolecular Polymers

The efficient collection of solar energy relies on the design and construction of well‐organized light‐harvesting systems. Herein we report that supramolecular phenanthrene polymers doped with pyrene are effective collectors of light energy. The linear polymers are formed through the assembly of short amphiphilic oligomers in water. Absorption of light by phenanthrene residues is followed by electronic energy transfer along the polymer over long distances (>100 nm) to the accepting pyrene molecules. The high efficiency of the energy transfer, which is documented by large fluorescence quantum yields, suggests a quantum coherent process.     

The SCC-DFTB method and its application to biological systems

The Self-consistent charge density functional tight-binding (SCC-DFTB) is an approximate quantum chemical method derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy expression. Here, we review in detail the application of SCC-DFTB to biological systems and several extensions of the original formalism. The biological systems discussed turn out to be a challenge for DFT due to the occurrence of weak binding forces and charge transfer problems, both of which are not properly described by recent DFT-GGA functionals. Possible solutions and alternative strategies are presented and the role of SCC-DFTB in a general quantum chemical approach to biological systems is discussed     

Dissipation of classical energy in nonlinear quantum systems

We show using two simple nonlinear quantum systems that the infinite set of quantum dynamical variables, as introduced in quantized Hamilton dynamics [O. V. Prezhdo and Y. V. Pereverzev, J. Chem. Phys. 113, 6557 (2000)], behave as a thermostat with respect to the finite number of classical variables. The coherent classical component of the evolution decays by coupling to the chaotic quantum reservoir. The classical energy, understood as the part of system energy expressible through the average values of coordinates and momenta, is transferred to the quantum energy expressible through the higher moments of coordinates and momenta and other quantum variables. At long times, the classical variables reach equilibrium, and the classical energy fluctuates around the equilibrium value. These phenomena are illustrated with the exactly solvable Jaynes-Cummings model and a nonlinear oscillator.     

Some aspects of photochemical systems for direct light-induced hydrogen production

Various possible pathways for photochemical conversion of light energy, including light-induced electron transfer and hydride transfer, are described. Several problems diminishing the photoconversion efficiency as well as side reactions affecting the stability of these systems are discussed. Oxidation of photosensitizers by singlet oxygen as well as attack by OH radicals is supposed to be the main degradation pathway for dyes and for the photoinduced reactions. The stability of viologens (acting as electron transfer agents) is mainly affected by hydrogenation, for which a reaction mechanism is presented. The dependence of rate constants on the free enthalpy of reaction is discussed with respect to quantum yields for light energy conversion. Following this, quantum yields of cyclic water splitting based on diffusion-controlled reactions are very low. Selective catalysis or vectorial processes (with a spatial charge separation) could enhance the quantum yields.     

Path integral calculation of free energies: quantum effects on the melting temperature of neon

The path integral formulation has been combined with several methods to determine free energies of quantum many-body systems, such as adiabatic switching and reversible scaling. These techniques are alternatives to the standard thermodynamic integration method. A quantum Einstein crystal is used as a model to demonstrate the accuracy and reliability of these free energy methods in quantum simulations. Our main interest focuses on the calculation of the melting temperature of Ne at ambient pressure, taking into account quantum effects in the atomic dynamics. The free energy of the solid was calculated by considering a quantum Einstein crystal as reference state, while for the liquid, the reference state was defined by the classical limit of the fluid. Our findings indicate that, while quantum effects in the melting temperature of this system are small, they still amount to about 6% of the melting temperature, and are therefore not negligible. The particle density as well as the melting enthalpy and entropy of the solid and liquid phases at coexistence is compared to results obtained in the classical limit and also to available experimental data.     

CdTe量子点-罗丹明6G荧光共振能量转移体系的构建及其应用研究

采用巯基化合物修饰的CdTe量子点构建了量子点(供体)-罗丹明6G(受体)荧光共振能量转移体系, 研究了CdTe量子点与牛血清白蛋白(BSA)的相互作用. 结果表明, CdTe量子点与BSA相互作用后提高了CdTe量子点-罗丹明6G 体系的荧光共振能量转移(FRET)效率, 减小了CdTe量子点和罗丹明6G分子间的距离(r), 证实BSA是通过其色氨酸(Trp)残基与CdTe量子点表面金属发生配位作用而直接结合到量子点表面的.