Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.     

Validation of Molecular Simulation: An Overview of Issues

Computer simulation of molecular systems enables structure–energy–function relationships of molecular processes to be described at the sub‐atomic, atomic, supra‐atomic, or supra‐molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Q^exp of experimentally observable quantities Q. One must consider 1) the accuracy of Q^exp, 2) the accuracy of the function Q( r ^N) used to calculate a Q‐value based on a molecular configuration r ^N of N particles, 3) the sensitivity of the function Q( r ^N) to the configuration r ^N, 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.     

Tunnelling junctions with additional degrees of freedom: An extended toolbox of scanning probe microscopy

Considering studies of molecular adsorption we review recent developments in the field of scanning probe microscopy and in particular in scanning tunnelling microscopy, concentrating on the progress that has been achieved by controlled decoration of the microscope tip. A view is presented according to which the tip decoration generally introduces additional degrees of freedom into the scanning junction and thus extends its functionality. In particular tips decorated with atomic point-like particles may attain the additional function of a force sensor which is realized through the degrees of freedom associated with the relative position of the decorating probe-particle with respect to the tip. It is shown how the force sensor function of such tips helps when studying large molecular adsorbates. Further prospects of more complex junctions equipped with numerous internal degrees of freedom are discussed. It is argued that the main problem impeding the utilization of such junctions is related to their control. An approach towards a higher degree of control is presented that is based on the analysis of single molecule manipulation experiments.     

Complex molecular assemblies at hand via interactive simulations

Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low‐resolution coarse‐grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well‐balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all‐atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N‐ethylmaleimide‐sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid–protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle‐based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Block‐adaptive quantum mechanics: An adaptive divide‐and‐conquer approach to interactive quantum chemistry

We present a novel Block‐Adaptive Quantum Mechanics (BAQM) approach to interactive quantum chemistry. Although quantum chemistry models are known to be computationally demanding, we achieve interactive rates by focusing computational resources on the most active parts of the system. BAQM is based on a divide‐and‐conquer technique and constrains some nucleus positions and some electronic degrees of freedom on the fly to simplify the simulation. As a result, each time step may be performed significantly faster, which in turn may accelerate attraction to the neighboring local minima. By applying our approach to the nonself‐consistent Atom Superposition and Electron Delocalization Molecular Orbital theory, we demonstrate interactive rates and efficient virtual prototyping for systems containing more than a thousand of atoms on a standard desktop computer. © 2012 Wiley Periodicals, Inc.     

Computational Characterization of Nanosystems

Nanosystems play an important role in many applications. Due to their complexity, it is challenging to accurately characterize their structure and properties. An important means to reach such a goal is computational simulation, which is grounded on ab initio electronic structure calculations. Low scaling and accurate electronic-structure algorithms have been developed in recent years. Especially, the efficiency of hybrid density functional calculations for periodic systems has been significantly improved. With electronic structure information, simulation methods can be developed to directly obtain experimentally comparable data. For example, scanning tunneling microscopy images can be effectively simulated with advanced algorithms. When the system we are interested in is strongly coupled to environment, such as the Kondo effect, solving the hierarchical equations of motion turns out to be an effective way of computational characterization. Furthermore, the first principles simulation on the excited state dynamics rapidly emerges in recent years, and nonadiabatic molecular dynamics method plays an important role. For nanosystem involved chemical processes, such as graphene growth, multiscale simulation methods should be developed to characterize their atomic details. In this review, we review some recent progresses in methodology development for computational characterization of nanosystems. Advanced algorithms and software are essential for us to better understand of the nanoworld.     

Environmental Effects in Computational Spectroscopy: Accuracy and Interpretation

Spectroscopic techniques are valuable tools for understanding the structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devoted to the development of new experimental techniques for improving the intrinsic resolution of different spectra. However, the subtle interplay of several different effects acting at different length and time scales still makes the interpretation and analysis of such spectra a very difficult task. In this respect, computational spectroscopy is becoming a needful and versatile tool for the assignment and interpretation of experimental spectra. It is in fact possible nowadays to model with relatively high accuracy the physical–chemical properties of complex molecules in different environments, and to link spectroscopic evidence directly to the structural and dynamical properties of optically or magnetically active solvated probes. In this Review, significant steps toward the simulation of entire spectra in condensed phases are presented together with some basic aspects of computational spectroscopy, which highlight how intramolecular and intermolecular degrees of freedom influence several spectroscopic parameters.     

Conformational and electronic properties of a microperoxidase in aqueous solution: a computational study.

A theoretical study of the conformational properties of a small heme peptide in aqueous solution is carried out by classical, long-timescale molecular dynamics simulations. The electronic properties of this species, that is, the relative energies of its excited electronic states and the redox potential, are reproduced and related to the conformational behavior using the perturbed matrix method and basic statistical mechanics. Our results show an interesting coupling between the conformational transitions and the electronic properties. These investigations, beyond the biophysically relevant results addressing the long-standing question of the actual role of the enzyme structure on the enzyme activity, are also of some methodological interest since they offer a further computational perspective for including the electronic degrees of freedom into the modeling of rather complex molecular systems.     

tCONCOORD-GUI: visually supported conformational sampling of bioactive molecules

Conformational flexibility of bioactive molecules poses a major challenge to computational biology. tCONCOORD generates structure ensembles based on geometrical considerations and has been successfully applied to predict protein conformational flexibility and essential degrees of freedom. We have now developed a graphical user interface (GUI) for tCONCOORD, which substantially facilitates the simulation setup and provides valuable insights into the structure analysis and constraint definition process in tCONCOORD. Moreover, users can influence the constraint definition process by interactively turning interactions on and off, defining completely rigid or flexible regions, or by applying artifical constraints that cause a biased sampling of the conformational space. This interface offers a versatile environment not only for the setup and analysis of tCONCOORD simulations, but also for molecular modeling and structure analysis in general. Both tCONCOORD* and the tCONCOORD-GUI(dagger) are distributed freely.     

利用基于直接动力学的轨线面跳跃方法处理非绝热过程

势能面交叉引起的非绝热过程广泛存在于光化学和光物理中。对这一过程进行描述是理论化学的重要挑战之一。非绝热过程涉及原子核与电子之间的耦合运动,因此量子化学的基本假设之一"玻恩-奥本海默"近似被打破,所以对其进行描述需要发展新的动力学理论方法。在这些方法中,Tully发展的最少轨线面跳跃方法凭借易于程序化、便于计算等优点已经发展成为处理非绝热问题的主要动力学方法之一。其中原子核以经典的方式在单一势能面上进行演化,电子以量子的方式沿着同一轨线进行演化。在整个演化过程中,非绝热跃迁通过轨线在不同势能面间的跃迁来描述,其中跳跃发生的几率与电子的演化有关。如果将该方法与从头算直接动力学相结合,可以在全原子水平上研究实际分子体系的非绝热动力学,给出其激发态寿命、非绝热动力学中分子的主要运动方式、反应通道以及分支比等重要信息。本文旨在讨论最少面跳跃直接动力学方法研究非绝热问题的一些进展,包括动力学基本理论,特别关注将最少面跳跃方法和直接动力学结合的数值实现细节,同时讨论该方法在研究实际体系当中的一些应用,并对轨线面跳跃方法下一步发展的一些方向进行合理的展望。     

Supra‐dendron Gelator Based on Azobenzene–Cyclodextrin Host–Guest Interactions: Photoswitched Optical and Chiroptical Reversibility

A novel amphiphilic dendron ( AZOC₈GAc ) with three l ‐glutamic acid units and an azobenzene moiety covalently linked by an alkyl spacer has been designed. The compound formed hydrogels with water at very low concentration and self‐assembled into chiral‐twist structures. The gel showed a reversible macroscopic volume phase transition in response to pH variations and photo‐irradiation. During the photo‐triggered changes, although the gel showed complete reversibility in its optical absorptions, only an incomplete chiroptical property change was achieved. On the other hand, the dendron could form a 1:1 inclusion complex through a host–guest interaction with α‐cyclodextrin (α‐CD), designated as supra‐dendron gelator AZOC₈GAc/α‐CD . The supra‐dendron showed similar gelation behavior to that of AZOC₈GAc , but with enhanced photoisomerization‐transition efficiency and chiroptical switching capacity, which was completely reversible in terms of both optical and chiroptical performances. The self‐assembly of the supra‐dendron is a hierarchical or multi‐supramolecular self‐assembling process. This work has clearly illustrated that the hierarchical and multi‐supramolecular self‐assembling system endows the supramolecular nanostructures or materials with superior reversible optical and chiroptical switching.     

Path Integral Molecular Dynamics of Liquid Water in a Mean-Field Particle Reservoir

We present a simulation scheme for path integral simulation of molecular liquids where a small open region is embedded in a large reservoir of non interacting point-particles. The scheme is based on the latest development of the adaptive resolution technique AdResS and allows for the space-dependent change of molecular resolution from a path integral representation with 120 degrees of freedom to a point particle that does not interact with other molecules and vice versa. The method is applied to liquid water and implies a sizable gain regarding the request of computational resources compared to full path integral simulations. Given the role of water as universal solvent with a specific hydrogen bonding network, the path integral treatment of water molecules is important to describe the quantum effects of hydrogen atoms’ delocalization in space on the hydrogen bonding network. The method presented here implies feasible computational efforts compared to full path integral simulations of liquid water which, on large scales, are often prohibitive.     

Bayesian inference of conformational state populations from computational models and sparse experimental observables

We present a Bayesian inference approach to estimating conformational state populations from a combination of molecular modeling and sparse experimental data. Unlike alternative approaches, our method is designed for use with small molecules and emphasizes high‐resolution structural models, using inferential structure determination with reference potentials, and Markov Chain Monte Carlo to sample the posterior distribution of conformational states. As an application of the method, we determine solution‐state conformational populations of the 14‐membered macrocycle cineromycin B, using a combination of previously published sparse Nuclear Magnetic Resonance (NMR) observables and replica‐exchange molecular dynamic/Quantum Mechanical (QM)‐refined conformational ensembles. Our results agree better with experimental data compared to previous modeling efforts. Bayes factors are calculated to quantify the consistency of computational modeling with experiment, and the relative importance of reference potentials and other model parameters. © 2014 Wiley Periodicals, Inc.     

Ab initio simulations of two‐dimensional electronic spectra: The SOS//QM/MM approach

Two‐dimensional electronic spectroscopy (2DES) is a cutting‐edge technique for investigating with high temporal resolution energy transfer, structure, and dynamics in a wide range of systems in physical chemistry, energy sciences, biophysics, and biocatalysis. However, the interpretation of 2DES is challenging and requires computational modeling. This perspective provides a roadmap for the development of computational tools that could be routinely applied to simulate 2DES spectra of multichromophoric systems active in the UV region (2DUV) using state‐of‐the‐art ab initio electronic structure methods within a quatum mechanics/molecular mechanics (QM/MM) scheme and the sum‐over‐states (SOS) approach (here called SOS//QM/MM). Multiconfigurational and multireference perturbative methods, such as the complete active space self‐consistent field and second‐order multireference perturbation theory (CASPT2) techniques, can be applied to reliably calculate the electronic properties of multichromophoric systems. Hybrid QM/MM method and molecular dynamics techniques can be used to assess environmental and conformational effects, respectively, that shape the 2D electronic spectra. DNA and proteins are important biological targets containing UV chromophores. We report ab initio simulation of 2DUV spectra of a cyclic tetrapeptide containing two interacting aromatic side chains, a model system for the study of protein structure and dynamics by means of 2DUV spectroscopy. © 2013 Wiley Periodicals, Inc.     

Quantum wavepacket ab initio molecular dynamics: generalizations using an extended Lagrangian treatment of diabatic states coupled through multireference electronic structure

We present a generalization to our previously developed quantum wavepacket ab initio molecular dynamics (QWAIMD) method by using multiple diabatic electronic reduced single particle density matrices, propagated within an extended Lagrangian paradigm. The Slater determinantal wavefunctions associated with the density matrices utilized may be orthogonal or nonorthogonal with respect to each other. This generalization directly results from an analysis of the variance in electronic structure with quantum nuclear degrees of freedom. The diabatic electronic states are treated here as classical parametric variables and propagated simultaneously along with the quantum wavepacket and classical nuclei. Each electronic density matrix is constrained to be N-representable. Consequently two sets of new methods are derived: extended Lagrangian-QWAIMD (xLag-QWAIMD) and diabatic extended Lagrangian-QWAIMD (DxLag-QWAIMD). In both cases, the instantaneous potential energy surface for the quantum nuclear degrees of freedom is constructed from the diabatic states using an on-the-fly nonorthogonal multireference formalism. By introducing generalized grid-based electronic basis functions, we eliminate the basis set dependence on the quantum nucleus. Subsequent reuse of the two-electron integrals during the on-the-fly potential energy surface computation stage yields a substantial reduction in computational costs. Specifically, both xLag-QWAIMD and DxLag-QWAIMD turn out to be about two orders of magnitude faster than our previously developed time-dependent deterministic sampling implementation of QWAIMD. Energy conservation properties, accuracy of the associated potential surfaces, and vibrational properties are analyzed for a family of hydrogen bonded systems.     

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation,validation, and benchmarks

Presented is the implementation of the Drude force field in the open‐source OpenMM simulation package allowing for access to graphical processing unit (GPU) hardware. In the Drude model, electronic degrees of freedom are represented by negatively charged particles attached to their parent atoms via harmonic springs, such that extra computational overhead comes from these additional particles and virtual sites representing lone pairs on electronegative atoms, as well as the associated thermostat and integration algorithms. This leads to an approximately fourfold increase in computational demand over additive force fields. However, by making the Drude model accessible to consumer‐grade desktop GPU hardware it will be possible to perform simulations of one microsecond or more in less than a month, indicating that the barrier to employ polarizable models has largely been removed such that polarizable simulations with the classical Drude model are readily accessible and practical.     

Closing the Nanographene Gap: Surface‐Assisted Synthesis of Peripentacene from 6,6′‐Bipentacene Precursors

The thermally induced cyclodehydrogenation reaction of 6,6′‐bipentacene precursors on Au(111) yields peripentacene stabilized by surface interactions with the underlying metallic substrate. STM and atomic‐resolution non‐contact AFM imaging reveal rectangular flakes of nanographene featuring parallel pairs of zig‐zag and armchair edges resulting from the lateral fusion of two pentacene subunits. The synthesis of a novel molecular precursor 6,6′‐bipentacene, itself a synthetic target of interest for optical and electronic applications, is also reported. The scalable synthetic strategy promises to afford access to a structurally diverse class of extended periacenes and related polycyclic aromatic hydrocarbons as advanced materials for electronic, spintronic, optical, and magnetic devices.     

Solvent Extraction: Structure of the Liquid–Liquid Interface Containing a Diamide Ligand

Knowledge of the (supra)molecular structure of an interface that contains amphiphilic ligand molecules is necessary for a full understanding of ion transfer during solvent extraction. Even if molecular dynamics already yield some insight in the molecular configurations in solution, hardly any experimental data giving access to distributions of both extractant molecules and ions at the liquid–liquid interface exist. Here, the combined application of X‐ray and neutron reflectivity measurements represents a key milestone in the deduction of the interfacial structure and potential with respect to two different lipophilic ligands. Indeed, we show for the first time that hard trivalent cations can be repelled or attracted by the extractant‐enriched interface according to the nature of the ligand.