International Journal of Quantum Chemistry

Cover image for Vol. 115 Issue 5

Early View (Online Version of Record published before inclusion in an issue)

Online ISSN: 1097-461X

Associated Title(s): Journal of Computational Chemistry

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  1. 1 - 36
  1. Perspective

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      How quantum chemistry can solve fundamental problems in bioenergetics

      Margareta R. A. Blomberg

      Article first published online: 24 JAN 2015 | DOI: 10.1002/qua.24868

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      Cellular energy conservation and energy storage processes are important in all forms of life. Quantum chemical calculations can provide fundamental insight into the mechanisms of enzymes involved in cellular energy conservation. Large molecular models of the active sites of such enzymes are used to construct free energy profiles. From the energy profiles, conclusions are drawn about mechanisms and structures, and experimental puzzles are solved.

  2. Full Papers

    1. Application of Löwdin's canonical orthogonalization method to the Slater-type orbital configuration-interaction basis set

      Li Guang Jiao and Yew Kam Ho

      Article first published online: 24 JAN 2015 | DOI: 10.1002/qua.24867

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      The Slater-type orbital configuration-interaction basis functions are easily linearly dependent in the large-number basis calculation of atomic systems. It is shown that Löwdin's canonical orthogonalization method is a powerful method to overcome such problem without using extended precision arithmetic. This article discusses the implementation of Löwdin's canonical orthogonalization method in different arithmetic precisions and demonstrates the feasibility of applying this method to the over-redundant basis calculations of two-electron atoms.

  3. Review

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      Magic state distillation and gate compilation in quantum algorithms for quantum chemistry

      Colin J. Trout and Kenneth R. Brown

      Article first published online: 24 JAN 2015 | DOI: 10.1002/qua.24856

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      Quantum chemistry algorithms on a quantum computer map the molecular Hamiltonian to a spin Hamiltonian. The dynamics of the Hamiltonian are then simulated using a set of elementary operations. Fault-tolerant protocols limit the set of operations and implementation of certain operations requires ancillary resource states, known as magic states. Recent developments that have improved the efficiency of magic state preparation and the compilation of arbitrary gates from discrete gate sets are reviewed.

  4. Full Papers

    1. Unique bonding pattern and resulting bond stretch isomerism in Be32−

      Tamal Goswami, Satadal Paul, Subhajit Mandal, Anirban Misra, Anakuthil Anoop and Pratim K. Chattaraj

      Article first published online: 20 JAN 2015 | DOI: 10.1002/qua.24866

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      Bond stretch isomerism is the phenomenon for which only the lengths of certain bonds are different in the isomers. The short-bond and long-bond isomers of inline image are investigated by means of density functional theory and highly accurate ab initio techniques. Both isomeres occupy minima in the potential enerdy surface and their differences are apparent in their molecular orbital-structure and bonding patterns. The short bond isomer shows an unusual bent-bond.

  5. Reviews

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      The bonding characteristics, electronic and magnetic properties of organometallic sandwich clusters and nanowires

      Xiaojing Yao, Xiuyun Zhang and Jinlan Wang

      Article first published online: 20 JAN 2015 | DOI: 10.1002/qua.24843

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      Organometallic sandwich compounds, comprised of organic molecules and metal atoms, have been receiving extensive attention recently due to their potential applications in wide range of fields spanning from nanocomposites to optoelectronic and biological sensors. This article reviews the important research advances, obtained recently by both experimental and theoretical approaches, on various organometallic sandwich clusters and molecular wires, and discuss their stability, bonding characteristics, molecular magnetism, electronic and transport properties.

  6. Full Papers

    1. Entanglement creation in Compton scattering of neutrons on protons and its possible energetic consequences

      Erik B. Karlsson

      Article first published online: 12 JAN 2015 | DOI: 10.1002/qua.24862

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      The possible energetic consequences of quantum entanglement are investigated, using p-n scattering as an example. It is first calculated (for the first time for a realistic case) how the entanglement arises during the interaction of the neutron and the proton and how it decays with the separation of the particles. In the entanglement process, energy is lost through virtual excitation of a compound deuteron state, resulting in a lowering of energy.

    2. Density functional study of organocatalytic mannich-type reactions: Insight into reverse diastereoselectivities arising from catalysts with different scaffolds

      Changke Tian, Aiping Fu, Chengyan Zhao, Hongliang Li, Zonghua Wang and Yunbo Duan

      Article first published online: 5 JAN 2015 | DOI: 10.1002/qua.24859

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      Quantum mechanical calculations play an important role in elucidating the reaction mechanism and stereoselectivity of organocatalyzed processes. The reverse diastereoselectivities arising from cyclic and acyclic α- and β-amino acids-promoted syn- and anti-selective Mannich reactions can be tested by means of density functional theory calculations. Tuning the distance between the bifunctional groups in the catalysts can help to control the reaction selectivity and consequently achieve different isomers.

    3. Electronic properties and 1/3 magnetization plateau of the S=1/2 magnetism Cu3(P2O6OH)2

      Long-Juan Kong, Guang-Hua Liu, Yu Zhang and Ling Qiang

      Article first published online: 24 DEC 2014 | DOI: 10.1002/qua.24861

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      One-dimensional magnetic materials characterized by linear spin chain structures yield great promises in several technological applications. The infinite time-evolving block decimation (iTEBD) algorithm is used to calculate magnetization, bipartite entanglement, and the nearest-neighbor correlations in the copper hydroxydiphosphate, Cu3(P2O6OH)2. Distinctive magnetization plateaus accompanied with some interesting bipartite entanglement and correlation plateaus are observed at T=0 k in the thermodynamic limit.

    4. Adaptive machine learning framework to accelerate ab initio molecular dynamics

      Venkatesh Botu and Rampi Ramprasad

      Article first published online: 23 DEC 2014 | DOI: 10.1002/qua.24836

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      The dynamical atomic-level evolution of typical chemical processes extends to timescales longer than nanoseconds—hard to access routinely using present ab initio methods. Here, an adaptive machine learning framework is proposed to significantly accelerate ab initio molecular dynamics simulations. The scheme learns to predict energies and atomic forces with unprecedented speed and accuracy from an initial ab initio dataset, and systematically expands its predictive capability on-the-fly by including newly encountered chemical environments in its training.

    5. Molecular insight into the interaction mechanisms of amino-2H-imidazole derivatives with BACE1 protease: A QM/MM and QTAIM study

      Esteban Gabriel Vega-Hissi, Rodrigo Tosso, Ricardo Daniel Enriz and Lucas Joel Gutierrez

      Article first published online: 23 DEC 2014 | DOI: 10.1002/qua.24854

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      Secretases have been identified as promising instruments against Alzheimer's disease. Molecular modeling provides accurate description of the binding interactions between two amino-2H-imidazole inhibitors to β-secretase. The binding affinity of these compounds is mostly related to the amino-2H-imidazole core, which interacts tightly with the aspartate dyad of the active site. © 2014 Wiley Periodicals, Inc.

  7. Tutorial Reviews

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      Effective quantum electrodynamics hamiltonians: A tutorial review

      Wenjian Liu

      Article first published online: 23 DEC 2014 | DOI: 10.1002/qua.24852

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      An effective quantum electrodynamics Hamiltonian incorporating all virtual pair effects can be derived both diagrammatically and algebraically. It serves as the basis for “with-pair relativistic quantum chemistry”. Such extension of the theoretical framework of relativistic quantum chemistry represents a conceptually important step for going beyond the no-pair approximation that has been prevailing in relativistic electronic structure calculations of molecular systems.

  8. Software News & Updates

    1. XMVB 2.0: A new version of Xiamen valence bond program

      Zhenhua Chen, Fuming Ying, Xun Chen, Jinshuai Song, Peifeng Su, Lingchun Song, Yirong Mo, Qianer Zhang and Wei Wu

      Article first published online: 20 DEC 2014 | DOI: 10.1002/qua.24855

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      A new version of Xiamen Valence Bond program, XMVB 2.0, is described in this article. In XMVB 2.0, several newly developed algorithms for orbital optimization in Valence Bond (VB) SCF framework are released. Newly implemented ab initio VB methods, such as VBSCF(CAS), icVBPT2, VBPCM, VBECP, and DFVB are also presented. Finally, test calculations of several planar arenes with up to 18 active electrons are performed with XMVB 2.0.

  9. Full Papers

    1. Dynamical entanglement of stretching–stretching and stretching–bending vibrations in SO2

      Liangjun Zhai and Yujun Zheng

      Article first published online: 17 DEC 2014 | DOI: 10.1002/qua.24848

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      The stretching–stretching and stretching–bending vibrations in the triatomic molecule SO2 are investigated as possible building blocks of a bipartite qubit system. The remaining stretching or bending vibrational mode is one resource of intramolecular decoherence. Because of the strong coupling between vibrational modes in SO2, the decoherence process of stretching–bending vibrations is very serious. The stretching–stretching vibrational entanglement is estimated to be more robust, and thus more suitable for the construction of qubits.

  10. Perspective

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      Toward the construction of parameter-free doubly hybrid density functionals

      Neil Qiang Su and Xin Xu

      Article first published online: 17 DEC 2014 | DOI: 10.1002/qua.24849

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      Doubly hybrid functionals present a new class of density functionals, which encompass the nonlocal orbital-dependent components not only in the exchange part but also in the correlation. Most current doubly hybrid functionals contain fitting parameters that are optimized against benchmark datasets, leading to generally good accuracies for the main group chemistry. However, more efforts shall be made toward the construction of parameter-free doubly hybrid functionals and the minimization of fractional charge and fractional spin errors.

  11. Full Papers

    1. A comprehensive study of the solvent effects on the cycloaddition reaction of diethyl azodicarboxylate and ethyl vinyl ether: Efficient implementation of QM and TD-DFT study

      Mohammad Khavani and Mohammad Izadyar

      Article first published online: 17 DEC 2014 | DOI: 10.1002/qua.24853

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      Parallel implementation of different methods of quantum mechanical and time-dependent DFT calculations provides an interesting new approach through which the investigation of the solvent effects on the reaction kinetics, excitation energies and some other aspects of the reaction is possible.

  12. Reviews

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      Theoretical investigation of NH3-SCR processes over zeolites: A review

      Yu Mao, Hai-Feng Wang and P. Hu

      Article first published online: 13 DEC 2014 | DOI: 10.1002/qua.24844

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      The selective catalytic reduction of NOx compounds with NH3 as reductant is a popular research topic. Zeolites have been proven to be efficient catalysts for this process. However, due to their structural complexity, the intrinsic mechanism of this reaction is still not well understood. This review provides a summary of the latest efforts to shine a light into this process using quantum chemical methods.

  13. Full Papers

    1. A theoretical investigation on palladium-catalyzed one-pot coupling of aryl iodides, alkynes, and amines through C[BOND]N bond cleavage for the synthesis of indole derivatives

      Nan Lu and Huatian Wang

      Article first published online: 13 DEC 2014 | DOI: 10.1002/qua.24842

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      Density Functional Theory provides insight into the pathways for C-N bond cleavage and amination catalyzed by cyclopentadiene–phosphine ligand – Palladium complexes (L1Pd0). The role of Pd is affected by the coordination ability of different oxidation state. The high selectivity of ligant L1 can be explained in terms of different electron distribution in C-N bond cleavage and amination steps.

    2. Quantum control of electron-proton symmetry breaking in dissociative ionization of H2 by intense laser pulses

      Mohammad Noh Daud, Huizhong Lu, Szczepan Chelkowski and Andre D. Bandrauk

      Article first published online: 13 DEC 2014 | DOI: 10.1002/qua.24845

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      Dissociative ionization of H2 has been a subject of considerable interest in recent years. Intense few-cycle laser pulses provide dependable control over carrier-envelope phase, offering a systematic control of electrons localization during laser dissociation of molecules. This article discusses the breakup of the H2 into proton, electron and hydrogen atom. The direction of the emitted electron can be controlled by quantum simulations, moving in the opposite direction of the proton emission.

  14. Perspective

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      Orbital entanglement in quantum chemistry

      Katharina Boguslawski and Paweł Tecmer

      Article first published online: 13 DEC 2014 | DOI: 10.1002/qua.24832

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      Quantum information theory provides tools to quantify the interaction of orbitals and allows us to measure the correlation between orbital pairs beyond the qualitative picture of molecular orbital theory. Orbital entanglement offers an alternative perspective to well-established concepts in chemistry and facilitates an understanding of electronic structures and how they change in chemical processes.

  15. Reviews

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      Economical basis sets and their uses in ab initio calculations

      Rui-Qin Zhang and Wen-Jie Fan

      Article first published online: 8 DEC 2014 | DOI: 10.1002/qua.24830

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      The roles of the particular functions composing a basis set, including the polarization and diffuse functions, as well as the nature and environment of each atom in a molecule need to be considered to choose the most appropriate basis in ab initio calculations. The number and level of basis functions required to describe an atom should increase from left to right in terms of its appearance in the periodic table and the relative increase in electronegativity.

  16. Review

    1. State-to-state reaction dynamics for the reactions of atom N with radicals

      Xixi Hu, Changjian Xie and Daiqian Xie

      Article first published online: 6 DEC 2014 | DOI: 10.1002/qua.24839

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      In the cold dense clouds, the temperature is so low (10–100 K) that any reactions with a significant barrier can be excluded. Therefore, barrierless complex-forming reactions are fundamental in any astrochemical models and need to be modeled with high accuracy. This article reviews general strategies of constructing a potential energy surface and the Chebyshev real wave packet method, and summarizes the recent studies for the reactions of atomic N with radicals OH, CH, and C2.

  17. Perspective

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      Understanding the microsolvation of salts in molecular clusters

      Cheng-Wen Liu and Yi Qin Gao

      Article first published online: 3 DEC 2014 | DOI: 10.1002/qua.24827

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      The microsolvation of salts in water can be qualitatively understood using molecular cluster models. However, for large clusters the high-dimensional potential energy surface can be quite complex. The combination of enhanced molecular dynamics simulations and quantum chemical calculations can overcome this problem. The microsolvation of three alkali–halide ion pairs is used to illustrate this methodology, and lead the discussion on future works and challenges in modeling salt–water and salt–water–organic systems.

  18. Full Papers

    1. The effects of resonance delocalization and the extent of π system on ionization energies of model fluorescent proteins chromophores

      Julia Lazzari-Dean, Anna I. Krylov and Ksenia B. Bravaya

      Article first published online: 2 DEC 2014 | DOI: 10.1002/qua.24825

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      Redox-active fluorescent proteins (FPs) are significant to many bioimaging applications and protein engineering efforts. Theoretical studies reveal strong effects of the OH-group position and the size of the π- conjugated system on the relative energies of the ground and electron-detached states of the chromophores. The effects of phenolate OH-group position on vertical ionization/detachment energies, as well as spin and charge delocalization, highlight the importance of resonance stabilization and substituent electronegativity in determining oxidation energetics.

  19. Software News & Updates

    1. HONPAS: A linear scaling open-source solution for large system simulations

      Xinming Qin, Honghui Shang, Hongjun Xiang, Zhenyu Li and Jinlong Yang

      Article first published online: 2 DEC 2014 | DOI: 10.1002/qua.24837

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      HONPAS is an ab initio electronic structure program for linear scaling (O(N)) first-principles calculations of large complex systems using standard norm-conserving pseudopotentials, numerical atomic orbitals basis sets, and periodic boundary conditions.

  20. Reviews

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      Time-dependent wavepacket diffusion method and its applications in organic semiconductors

      Lu Han, Yaling Ke, Xinxin Zhong and Yi Zhao

      Article first published online: 2 DEC 2014 | DOI: 10.1002/qua.24833

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      In organic materials, the carrier-phonon interaction plays an important role for the carrier transport process. The time-dependent wavepacket diffusion (TDWPD) method has been developed to model carrier dynamics from coherent band-like to hopping-type regimes. Published results demonstrate that TDWPD can accurately predict the carrier dynamics of systems from small compounds to nanoscale materials including thousands of molecules. TDWPD can be effectively combined with electronic structure calculations and tackle realistic models of organic semiconductors.

  21. Full Papers

    1. Shannon entropy and many-electron correlations: Theoretical concepts, numerical results, and Collins conjecture

      Luigi Delle Site

      Article first published online: 28 NOV 2014 | DOI: 10.1002/qua.24823

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      Links between the electron density of DFT and the many-body wavefunctions/correlations are put forward in terms of encoding/decoding concepts of information theory. In particular, the concept of Shannon entropy can be employed into the development of electronic correlation functionals, and the Hohenberg−Kohn theorem be seen as a specific case of a more general encoding process.

  22. Reviews

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      Modeling the low frequency vibrational spectroscopy of the ionic solutions

      Ruiting Zhang, Zhijun Pan and Wei Zhuang

      Article first published online: 28 NOV 2014 | DOI: 10.1002/qua.24826

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      Low frequency vibration spectroscopy plays a unique role in studying the interaction between ions and water molecules. This review discusses some recent efforts in modeling and analyzing the low frequency vibration spectra of ionic solutions. Issues in current theoretical simulation and concerns for further investigations are also addressed.

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      Generalized time-dependent approaches to vibrationally resolved electronic and Raman spectra: Theory and applications

      Wanzhen Liang, Huili Ma, Hang Zang and Chuanxiang Ye

      Article first published online: 27 NOV 2014 | DOI: 10.1002/qua.24824

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      Vibronic spectroscopy involves simultaneous changes in the vibrational and electronic energy states of a molecule. Its calculation requires both the knowledge of quantum dynamics and advanced electronic structure theory. This review summarizes the general time-dependent approaches on a series of vibronic spectra with inclusion of Frank–Condon, Herzberg–Teller, and mode mixing effects. The numerical applications to one/two-photon absorption and emission, and Raman spectra are demonstrated.

  23. Software News & Updates

    1. LSQC: Low scaling quantum chemistry program

      Wei Li, Chihong Chen, Dongbo Zhao and Shuhua Li

      Article first published online: 27 NOV 2014 | DOI: 10.1002/qua.24831

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      LSQC is a low scaling quantum chemistry program for ab initio and DFT calculations of large systems. This program includes two methods, generalized energy-based fragmentation (GEBF) approach and cluster-in-molecule (CIM) approach. In the GEBF approach, the energy and properties of a large system can be obtained from the calculations of a series of subsystems. In the CIM approach, the electron correlation energy can be obtained from various clusters based on localized molecular orbitals.

  24. Full Papers

    1. Two-dimensional reactive scattering with transmitted quantum trajectories

      Chia-Chun Chou

      Article first published online: 24 NOV 2014 | DOI: 10.1002/qua.24828

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      Time-dependent reaction dynamics is studied by evolving an ensemble of transmitted quantum trajectories. Reflected trajectories are gradually removed during the ensemble evolution. This removal process avoids numerical instabilities 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.

  25. Perspectives

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      Polarizable force fields based on physical models and quantum chemical calculations

      Xingyong Wang, Tianying Yan and Jing Ma

      Article first published online: 20 NOV 2014 | DOI: 10.1002/qua.24829

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      Nonpolarizable force fields cannot guarantee the accurate calculation of optical dielectric constants. The parameterization of polarizable FFs is not trivial, but electrostatics approaches, like the FQ model, Drude model, and the ID model, and fragment-based low-scaling QM methods show great potential in the hands of the community of developers.

  26. Full Papers

    1. Stepwise hydration of phosphate anion: A microscopic theory connecting domain of instability and stability

      Arup Kumar Pathak

      Article first published online: 17 NOV 2014 | DOI: 10.1002/qua.24816

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      Present microscopic theory-based studies provide a robust scheme that connects domain of stability from the knowledge of the domain of instability as a function of coordinated water molecules. This scheme also helps to calculate vertical detachment energy of the hydrated cluster of phosphate anion over a wide range of cluster sizes, including the bulk.

  27. Perspective

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      Potential generation and path-integral Monte Carlo in study of microscopic superfluidity

      Tao Zeng, Hui Li and Pierre-Nicholas Roy

      Article first published online: 15 NOV 2014 | DOI: 10.1002/qua.24815

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      Microscopic superfluidity can be demonstrated in microscopic Andronikashvilli experiments. In theory, it can be modeled through simulations of quantum rotation of molecular rotors embedded in microscopic superfluids such as 4He and para-H2. The methodologies used in generating accurate rotor-solvent potential energy surfaces, and the path-integral Monte Carlo method that is used in the actual simulations, are reviewed in this article, which aims to serve as a mini tutorial review for the subject of microscopic superfluidity.

  28. Full Papers

    1. Fisher and Shannon information in orbital-free density functional theory

      Ágnes Nagy

      Article first published online: 15 NOV 2014 | DOI: 10.1002/qua.24812

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      Information theory concepts are getting traction in both physics and chemistry. Very relevant for density function theory is the relationship established between the quantum mechanical kinetic energy functional and Fisher information. The Shannon information has instead proved to be a very useful tool in analyzing atoms and molecules. In this article, the Euler equation (independent from the number of electrons) of the orbital-free density functional theory is reformulated with the Shannon and Fisher information.

  29. Reviews

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      Neural network-based approaches for building high dimensional and quantum dynamics-friendly potential energy surfaces

      Sergei Manzhos, Richard Dawes and Tucker Carrington

      Article first published online: 6 OCT 2014 | DOI: 10.1002/qua.24795

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      Neural Network-based methods for potential energy surface (NN PESs) fitting can be considered “black box” in that they do not impose any predefined functional form, and thus are very portable. However, their main disadvantage is that their accuracy is guaranteed only for a sufficiently high density of fitting points. In this case, NN PESs are arguably very accurate for small molecules and as good as other fitting methods for larger molecules.

  30. Perspective

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      Phase/current information descriptors and equilibrium states in molecules

      Roman F. Nalewajski

      Article first published online: 10 SEP 2014 | DOI: 10.1002/qua.24750

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      Information-theoretic description of electronic states requires the classical (probability) descriptors and their nonclassical (current) complements. The unconstrained extremum of the resultant entropy/information content determines the phase-transformed equilibrium state, which differs from the stationary (zero-current) state of quantum mechanics. The nonclassical supplements to the familiar classical measures, global (Shannon), and local (Fisher), are designed and current promotion of molecular fragments is explored. This fully quantum information-theoretic approach generates thermodynamic perspective on time evolution of equilibrium states.

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