Radical pair recombination reactions are known to be sensitive to extremely weak magnetic fields, and can therefore be said to function as molecular magnetoreceptors. The classic example is a carotenoid-porphyrin-fullerene (C+PF-) radical pair that has been shown to provide a "proof-of-principle" for the operation of a chemical compass [K. Maeda et al., Nature 453, 387 (2008)]. Previous simulations of this radical pair have employed semiclassical approximations, which are routinely applicable to its 47 coupled electronic and nuclear spins. However, calculating the exact quantum mechanical spin dynamics presents a significant challenge, and has not been possible before now. Here we use a recently developed method to perform numerically converged simulations of the C+PF- quantum mechanical spin dynamics, including all coupled spins. Comparison of these quantum mechanical simulations with various semiclassical approximations reveals that, while it is not perfect, the best semiclassical approximation does capture essentially all of the relevant physics in this problem.
One of the principal models of magnetic sensing in migratory birds rests on the quantum spin-dynamics of transient radical pairs created photochemically in ocular cryptochrome proteins. We consider here the role of electron spin entanglement and coherence in determining the sensitivity of a radical pair-based geomagnetic compass and the origins of the directional response. It emerges that the anisotropy of radical pairs formed from spin-polarized molecular triplets could form the basis of a more sensitive compass sensor than one founded on the conventional hyperfine-anisotropy model. This prop…
We examine the effect of structural disorder and dynamical lattice fluctuation on charge migration dynamics starting from a birth of local exciton in a quantum network of molecular aggregates by using model Hamiltonians having complicate interactions. Here all monomers are supposed to be the same for simplicity. A natural use of inherent sparsity of Hamiltonian matrix allows us an investigation of essential features in quantum network dynamics accompanied with a fluctuation of interaction. Variation of disorder parameter, kinetic energy and effective mass of monomers in electron dynamics calcu…
A class of preconditioners is introduced to enhance geometry optimisation and transition state search of molecular systems. We start from the Hessian of molecular mechanical terms, decompose it and retain only its positive definite part to construct a sparse preconditioner matrix. The construction requires only the computation of the gradient of the corresponding molecular mechanical terms that are already available in popular force field software packages. For molecular crystals, the preconditioner can be combined straightforwardly with the exponential preconditioner recently introduced for p…
Building on Paper I of this series, which introduced path integral Monte Carlo (PIMC) estimators for the derivative of the potential of mean force (PMF), we propose two path integral molecular dynamics (PIMD) integrators that can make use of these estimators. These integrators, c-OBABO and c-BAOAB, are based on the path integral Langevin equation (PILE) integrator, which has seen widespread success in PIMD applications, but they include support for holonomic constraints. When the reaction coordinate is the distance between two centers of mass, we find that several exact expressions are accessi…
"Alchemical" interpolation paths, i.e.~coupling systems along fictitious paths that without realistic correspondence, are frequently used within materials and molecular modeling and simulation protocols for the estimation of relative changes in state functions such as free energies. We discuss alchemical changes in the context of quantum chemistry, and present illustrative numerical results for the changes of HOMO eigenvalues of the He atom due to a linear alchemical teleportation---the simultaneous annihilation and creation of nuclear charges at different locations. To demonstrate the predict…
Coupling Quantum Mechanical Modeling and Molecular Dynamics on Heterogeneous Supercomputers for Studying Distal Mutation Effects on Drug Binding in HIV-1
RIKEN Center for Computational Science（理化学研究所计算科学中心）；INRIA（法国国家信息与自动化研究所）；University Grenoble Alpes（格勒诺布尔阿尔卑斯大学）
The chiral algebra of tetrahedral molecules, derived from Fischer projections, is discussed in the framework of quantum mechanics. A quantum chiral algebra is obtained whose operators, acting as rotations or inversions, commute with the Hamiltonian of the system. It is shown that energy and chirality eigenstates are strictly related through the Heisenberg relations, while chirality operators conserve parity eigenstates.
Machine learning approaches in drug discovery, as well as in other areas of the chemical sciences, benefit from curated datasets of physical molecular properties. However, there is a lack of sufficiently large data collections that include first-principle quantum chemical information on bioactive molecules, such as single-point electronic properties, quantum mechanical wave functions and density-functional theory (DFT) matrices. The open-access QMugs (Quantum-Mechanical Properties of Drug-like Molecules) dataset fills this void. The QMugs collection comprises quantum mechanical properties of m…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Le…
With the continuous growth of processing power for scientific computing, first principles Born-Oppenheimer molecular dynamics (MD) simulations are becoming increasingly popular for the study of a wide range of problems in materials science, chemistry and biology. Nevertheless, the computational cost still remains prohibitively large in many cases, particularly in comparison to classical MD simulations using empirical force fields. Here we show how to circumvent the major computational bottleneck in Born-Oppenheimer MD simulations arising from the self-consistent-charge optimization. The optimi…
Using a new analytic quantum mechanical method based on Slater's Xalpha method, we show that a fairly accurate estimate of the total energy of a molecule can be obtained from the exact energies of its constituent atoms. The mean absolute error in the total energies thus determined for the G2 set of 56 molecules is about 16 kcal/mol, comparable to or better than some popular pure and hybrid density functional models.
Manipulating and coupling molecule gears is the first step towards realizing molecular-scale mechanical machines. Here, we theoretically investigate the behavior of such gears using molecular dynamics simulations. Within a nearly rigid-body approximation we reduce the dynamics of the gears to the rotational motion around the orientation vector. This allows us to study their behavior based on a few collective variables. Specifically, for a single hexa (4-tert-butylphenyl) benzene molecule we show that the rotational-angle dynamics corresponds to the one of a Brownian rotor. For two such coupled…
We study the electrostatic potential of a molecular wire bridging two metallic electrodes in the limit of weak contacts. With the use of a tight-binding model including a fully three-dimensional treatment of the electrostatics of the molecular junction, the potential is shown to be poorly screened, dropping mostly along the entire molecule. In addition, we observe pronounced Friedel oscillations that can be related to the breaking of electron-hole symmetry. Our results are in semi-quantitative agreement with recent state-of-the-art ab initio calculations and point to the need of a three-dimens…
Seoul National University（首尔大学）；Kakao Corporation（Kakao公司）；Seoul National University of Science and Technology（首尔科学技术院）
A molecule is a complex of heterogeneous components, and the spatial arrangements of these components determine the whole molecular properties and characteristics. With the advent of deep learning in computational chemistry, several studies have focused on how to predict molecular properties based on molecular configurations. Message passing neural network provides an effective framework for capturing molecular geometric features with the perspective of a molecule as a graph. However, most of these studies assumed that all heterogeneous molecular features, such as atomic charge, bond length, o…
We show that the conductance $G$ of molecular tunnel junctions wherein the charge transport is dominated by a single energy level can be expressed in closed analytic form which is exact and valid at arbitrary temperature $T$ and model parameter values. On this basis, we show that the single-step tunneling mechanism is compatible with a continuous thermal transition from a weakly $T$-dependent $G$ at low $T$ (Sommerfeld regime) to a nearly exponential $1/T$-dependent $G$ at high $T$ (Arrhenius-like regime). We predict that this Sommerfeld-Arrhenius transition can be observed in real molecular j…
The excess free energy of a molecular cluster is a key quantity in models of the nucleation of droplets from a metastable vapour phase; it is often viewed as the free energy arising from the presence of an interface between the two phases. We show how this quantity can be extracted from simulations of the mechanical disassembly of a cluster using guide particles in molecular dynamics. We disassemble clusters ranging in size from 5 to 27 argon-like Lennard-Jones atoms, thermalised at 60 K, and obtain excess free energies, by means of the Jarzynski equality, that are consistent with previous stu…
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab initio (ai) quantum mechanical/molecular mechanics (QM/MM) level is still far too expensive. Semiempirical (SE) method can be hundreds or thousands of times faster than the ai methods. However, the accuracy of SE methods is often unsatisfactory, due to the approximations that have been adopted in these methods. In this work, we proposed a new method termed MBA…
Mechanical and thermodynamic routes to the liquid-liquid interfacial tension and mixing free energy by molecular dynamics
Osaka University（大阪大学）；Tohoku University（东北大学）；Osaka Metropolitan University（大阪公立大学）；Brunel University London（伦敦布鲁内尔大学）；Université Claude Bernard Lyon 1（里昂第一大学）；Tokyo University of Science（东京科学大学）
We present a quantum mechanical / molecular mechanics (QM/MM) to tackle chemical reactions with substantial molecular reorganization. For this, molecular dynamics simulations with smoothly switched interaction models are used to suggest suitable product states, whilst a Monte Carlo algorithm is employed to assess the reaction likeliness subject to energetic feasibility. As a demonstrator, we study the cross-linking of bisphenol F diglycidyl ether (BFDGE) and 4,6-diethyl-2-methylbenzene-1,3-diamine (DETDA). The modeling of epoxy curing was supplemented by Differential Scanning Calorimetry (DSC)…
We introduce and employ two QM:QM schemes (a quantum mechanical method embedded into another quantum mechanical method) and report their performance for the X23 set of molecular crystals. We furthermore present the theory to calculate the stress tensors necessary for the computation of optimized cell volumes of molecular crystals and compare all results to those obtained with various density functionals and more approximate methods. Our QM:QM calculations with PBE0:PBE+D3, PBE0:PBE+MBD, and B3LYP:BLYP+D3 yield at a reduced computational cost lattice energy errors close to the ones of the paren…
An evaluation of machine learning/molecular mechanics end-state corrections with mechanical embedding to calculate relative protein-ligand binding free energies
We have analyzed with pedagogical purposes the relation of the total densities of states (TDOS/PDOS/OPDOS) and molecular orbital diagrams (MOD) for single and isolated molecules of Water and Nitrogen. We use a calculation level HF/6-311G, spreading the energy eigenvalues around the TDOS spikes and using the Mulliken visual analysis in Multiwfn to showcase our findings. We discuss the possibility to use these electrons orbit population diagrams, in conjunction with the more intuitive MOD diagrams to teach the Quantum Mechanics of simple molecular isolated structures.
Vibrational Fingerprints of Strained Polymers: A Spectroscopic Pathway to Mechanical State Prediction
Hamburg University of Technology（汉堡大学）；Centre for Quantum Materials and Technologies（量子材料与技术中心）；Helmholtz-Zentrum Hereon（海德堡研究中心）；Institute for Interface Physics and Engineering（界面物理与工程研究所）；Institute of Polymers and Composites（聚合物与复合材料研究所）
Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to reveal the effect of hydroxyl radicals produced by the secondary effect of radiation. Previous studies address the problem with truncated DNA bases as ab-initio quantum simulation required to study such electronic spin dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid Quantum-Mechanical-Molecular-Mechanical simulation to study the interaction of OH radicals with guanine-deoxyribose-phosphate DNA molecular unit in the pre…
This paper addresses the three following questions. (i) How the structures of group and of chain of groups enter nuclear, atomic and molecular spectroscopy? (ii) How these structures can be exploited, in a quantum- mechanical framework, in the problems of state labelling and (external) symmetry breaking? (iii) How it is possible to associate a Wigner-Racah algebra to a group or a chain of groups for making easier the calculation of quantum-mechanical matrix elements? Numerous examples illustrate the philosophy of qualitative and quantitative applications to spectroscopy.
