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Entanglement and co-tunneling of two equivalent protons in hydrogen bond pairs

Zorka Smedarchina, Willem Siebrand, Antonio Fernández-Ramos
2018 Journal of Chemical Physics  
The method is applied to the molecule porphycene for which the observed tunneling splitting is calculated in satisfactory agreement with experiment, and the mechanism of double-proton tunneling is found  ...  The tunneling Hamiltonian has two imaginary modes (reaction coordinates) and a potential with a single maximum that may turn into a saddle-point of second order and two sets of (inequivalent) minima.  ...  A complete solution of the multidimensional vibrational Hamiltonian of a complex molecule with two tunneling coordinates far exceeds our present computational capabilities.  ... 
doi:10.1063/1.5000681 pmid:29544290 fatcat:aaogvewuu5eqjb6fsikz6oxofa

Helical [n]catamantanes and all-trans-perhydroacenic [n]perimantanes: structures and von Baeyer IUPAC numbering of carbon atoms

2013 ARKIVOC  
, and [n]perimantanes whose dualists are all-trans-perhydroacenes; general numbering schemes were derived for these compound classes.  ...  distinguished by the Balaban-Schleyer nomenclature system, substituted derivatives are to be described by the IUPAC von Baeyer nomenclature that attributes a unique number (locant) to each carbon atom within a molecule  ...  Columns D, H, L represent "concave bend corner atoms" on the outer upper path with numbers increasing stepwise by 4,0,4,0,… for increasing n.  ... 
doi:10.3998/ark.5550190.p008.352 fatcat:v6qwqvax7vgz3gcapncvlf64ru

CO2Molecule as a Quantum Realization of the1∶1∶2Resonant Swing-Spring with Monodromy

R. H. Cushman, H. R. Dullin, A. Giacobbe, D. D. Holm, M. Joyeux, P. Lynch, D. A. Sadovskií, B. I. Zhilinskií
2004 Physical Review Letters  
We study the quantum swing-spring formed by bending and symmetric stretching vibrations of the CO 2 molecule.  ...  We consider the wide class of systems modeled by an integrable approximation to the 3 degrees of freedom elastic pendulum with 1:1:2 resonance, or the swing-spring.  ...  The EM map of the more general Fermi model system with Þ 0 is qualitatively the same for all n and can be obtained by a small continuous deformation of the 0 case.  ... 
doi:10.1103/physrevlett.93.024302 pmid:15323921 fatcat:74ja7zdijzhrjbfqcbzvqmaygm

Chapter 3 Methods for Monte Carlo Simulations of Biomacromolecules [chapter]

Andreas Vitalis, Rohit V. Pappu
2009 Annual Reports in Computational Chemistry  
Detailed sections are provided dealing with the choice of degrees of freedom, the efficiencies of MC algorithms and algorithmic peculiarities, as well as the optimization of simple movesets.  ...  when used in conjunction with implicit solvation models or other coarse graining strategies.  ...  earlier versions of this package) that helped guide our thinking regarding Monte Carlo simulations.  ... 
doi:10.1016/s1574-1400(09)00503-9 pmid:20428473 pmcid:PMC2860296 fatcat:rogy3kwucbgovbjpv776jf3v5u

Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method

Chao Lu, Xubin Li, Dongsheng Wu, Lianqing Zheng, Wei Yang
2015 Journal of Chemical Theory and Computation  
To promote essential fluctuations to enhance sampling, a common strategy is to construct an expanded Hamiltonian through a series of Hamiltonian perturbations, for instance on certain interactions of focus  ...  Due to lack of active sampling of configuration response to perturbation transitions, it is challenging for common expanded Hamiltonian methods to robustly explore solvent mediated rare conformational  ...  Then the H λ Hamiltonian in Equation 7 is generalized to a new Hamiltonian: .  ... 
doi:10.1021/acs.jctc.5b00953 pmid:26636477 pmcid:PMC4968881 fatcat:rg26v74dnjerjdntvhwanos7vm

High-resolution infrared spectroscopy and analysis of the ν 2 /ν 4 bending dyad of ruthenium tetroxide

S. Reymond-Laruinaz, M. Faye, V. Boudon, D. Doizi, L. Manceron
2017 Journal of Molecular Spectroscopy  
RuO 4 is a heavy tetrahedral molecule of interest in several fields.  ...  We provide precise effective Hamiltonian parameters, including band centers and Coriolis interaction parameters.  ...  Two spectra were recorded, one with 5.44 m and 0.2 mbar sample pressure and a second with 19.04 m path length and the same pressure for a better recording of the weaker lines.  ... 
doi:10.1016/j.jms.2017.04.010 fatcat:vqxuoi42brfxpp3isuhn4x3dvy

Nonequilibrium Fermi golden rule for electronic transitions through conical intersections

Artur F. Izmaylov, David Mendive–Tapia, Michael J. Bearpark, Michael A. Robb, John C. Tully, Michael J. Frisch
2011 Journal of Chemical Physics  
The results of our model are found to agree well with those of quantum dynamics for a test set of systems: fulvene molecule, bis-methylene adamantane cation and its dimethyl derivative.  ...  The derived expression can be seen as a nonequilibrium generalization of the Fermi Golden Rule due to a nonequilibrium character of the initial photoinduced nuclear distribution.  ...  ., surface hopping), wave packet methods [5] [6] [7] , semi-classical 8 and general path-integral based approaches 9, 10 .  ... 
doi:10.1063/1.3667203 pmid:22191863 fatcat:jfo4bamg2rcabh5itxy7b4mjtu

Analog Quantum Approximate Optimization Algorithm [article]

Nancy Barraza, Gabriel Alvarado Barrios, Jie Peng, Lucas Lamata, Enrique Solano, Francisco Albarrán-Arriagada
2021 arXiv   pre-print
This algorithm provides an approximate result of optimization problems that may be developed during the coherence time of current quantum annealers on their way towards quantum advantage.  ...  We present an analog version of the quantum approximate optimization algorithm suitable for current quantum annealers.  ...  does not follow, in general, an adiabatic path.  ... 
arXiv:2112.07461v1 fatcat:z3pu3oltkfajfakxxkz6ehjaq4

Tunneling splitting in double-proton transfer: Direct diagonalization results for porphycene

Zorka Smedarchina, Willem Siebrand, Antonio Fernández-Ramos
2014 Journal of Chemical Physics  
A direct-dynamics study of proton transfer through water bridges in guanine and 7-azaindole  ...  The CDPT model consists of two identical interacting hydrogen bonds to provide a general description of the dynamics of correlated double-proton transfer that is valid for concerted as well as stepwise  ...  To achieve that, we use a model 2D Hamiltonian of the same symmetry as the porphycene molecule, which we generate from the calculated data of Sec. III and then diagonalize numerically.  ... 
doi:10.1063/1.4900717 pmid:25381519 fatcat:5ib4zq5tkjegziazg3vq4gfd4m

Attosecond streaking spectrum in the photoionization of the hydrogen molecular ion

Feng Wang, Kai Liu, Xiaofan Zhang, Zhe Wang, Meiyan Qin, Qing Liao, Peixiang Lu
2019 Physical Review A  
The 3MPPs are constructed by "chosen paths", a method of shortcuts to adiabaticity (STA), exhibiting a fast two-photon process.  ...  The present work may provide help for laboratory researchers in a robust separation of chiral molecules.  ...  This work was supported by National Natural Science Foundation of China (NSFC) (11675046), Program for Innovation Research of Science in Harbin Institute of Technology (A201412), and Postdoctoral Scientific  ... 
doi:10.1103/physreva.100.043405 fatcat:wztab3d3ynh3rk3m236tgpuisq

Excited-state double proton transfer of 1,8-dihydroxy-2-naphthaldehyde: A MS-CASPT2//CASSCF study

Bin-Bin Xie, Ke-Xin Wang, Pei-Ke Jia, Xiang-Yang Liu, Ganglong Cui
2022 Chinese Journal of Chemical Physics  
a stepwise ESDPT mechanism.  ...  The linear interpolated internal coordinate path connecting S1-KETO-1 (S1-KETO-2) and S1S0-KETO-1 (S1S0-KETO-2) is uphill with a barrier of ca. 12.0 kcal/mol, which will trap DHNA in the S1 state while  ...  On the basis of our computational results, the stepwise ESDPT mechanism was confirmed, which will finally generate S1-KETO-1 and S1-KETO-2, respectively.  ... 
doi:10.1063/1674-0068/cjcp2109163 fatcat:fupmfympibbnth36invsnuavva

Phase-space geometry and reaction dynamics near index 2 saddles

Gregory S Ezra, Stephen Wiggins
2009 Journal of Physics A: Mathematical and Theoretical  
We study the phase space geometry associated with index 2 saddles of a potential energy surface and its influence on reaction dynamics for n degree-of-freedom (DoF) Hamiltonian systems.  ...  In particular, we can identify a class of trajectories, which we refer to as "roaming trajectories", which are not associated with reaction along the classical minimum energy path (MEP).  ...  Acknowledgments SW acknowledges the support of the Office of Naval Research Grant No N00014-01-1-0769.  ... 
doi:10.1088/1751-8113/42/20/205101 fatcat:lgxr2jqxjrdqjofsgpkqkmjvgm

Studies of Proton Translocations in Biological Systems: Simulating Proton Transport in Carbonic Anhydrase by EVB-Based Models

Sonja Braun-Sand, Marek Strajbl, Arieh Warshel
2004 Biophysical Journal  
of PTR with significant activation barriers.  ...  It is concluded that this approach and the EVB-based model provide a reliable, effective, and general tool for studies of PTR in proteins.  ...  This case is less sensitive to the decrease of the pK a of the central H 3 O 1 because of the fact that the concerted path helps to overcome the barrier of the stepwise path.  ... 
doi:10.1529/biophysj.104.043257 pmid:15454425 pmcid:PMC1304648 fatcat:7guclmficvchrjmd4vqip2773m

Inverse Quantum Chemistry: Concepts and Strategies for Rational Compound Design [article]

Thomas Weymuth, Markus Reiher
2014 arXiv   pre-print
The rational design of molecules and materials is becoming more and more important.  ...  With the advent of powerful computer systems and sophisticated algorithms, quantum chemistry plays an important role in rational design.  ...  In such studies, von Lilienfeld and coworkers found that the path connecting any two molecules is generally not linear [96] .  ... 
arXiv:1401.1512v1 fatcat:dkbm2hlperd7ll2zvmfuwakm4u

Entropy Contributions to Transition State Modeling [chapter]

Kristof De Wispelaere, Louis Vanduyfhuys, Veronique Van Speybroeck
2018 Modelling and Simulation in the Science of Micro- and Meso-Porous Materials  
We also acknowledge all current and former CMM members for general discussions on this topic.  ...  Acknowledgements We thank the Foundation of Scientific Research -Flanders (FWO), the Research Board of Ghent University, BELSPO (IAP P7/05), the European Union's Horizon 2020 research and innovation programme  ...  Recently Ceriotti and co-workers developed a Python interface for using path integral MD simulations in combination with electronic structure programs. [98] 26 Another methods consists of generating quasi-classical  ... 
doi:10.1016/b978-0-12-805057-6.00006-5 fatcat:d3jjmbx4xzat7ahoeeul6ltilq
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