Interactive chemical reactivity exploration.

@article{Haag2014InteractiveCR,
  title={Interactive chemical reactivity exploration.},
  author={Moritz P. Haag and A. Vaucher and Ma{\"e}l Bosson and S. Redon and M. Reiher},
  journal={Chemphyschem : a European journal of chemical physics and physical chemistry},
  year={2014},
  volume={15 15},
  pages={
          3301-19
        }
}
  • Moritz P. Haag, A. Vaucher, +2 authors M. Reiher
  • Published 2014
  • Computer Science, Chemistry, Physics, Medicine
  • Chemphyschem : a European journal of chemical physics and physical chemistry
Elucidating chemical reactivity in complex molecular assemblies of a few hundred atoms is, despite the remarkable progress in quantum chemistry, still a major challenge. Black-box search methods to find intermediates and transition-state structures might fail in such situations because of the high-dimensionality of the potential energy surface. Here, we propose the concept of interactive chemical reactivity exploration to effectively introduce the chemist's intuition into the search process. We… Expand
Ab Initio Reactive Computer Aided Molecular Design.
  • T. Martínez
  • Chemistry, Medicine
  • Accounts of chemical research
  • 2017
TLDR
It is argued that due to recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within reach. Expand
Molecular Propensity as a Driver for Explorative Reactivity Studies
TLDR
Within the real-time quantum chemistry framework, an algorithm is developed that automatically detects and flags the predisposition of a molecular system to react across different electronic states in certain nuclear configurations or with other reactants present in the reaction liquor. Expand
Accelerating Wave Function Convergence in Interactive Quantum Chemical Reactivity Studies.
TLDR
This work introduces two schemes for SCF acceleration that provide a guess for the initial density matrix of the SCF procedure generated by extrapolation techniques and achieves speedups of up to 30% as a consequence of a reduced number of SCF iterations. Expand
The Exploration of Chemical Reaction Networks.
TLDR
The purpose of this overview is to categorize the problems that should be targeted and to identify the principle components and challenges of automated exploration machines so that the various existing approaches and future developments can be compared based on well-defined conceptual principles. Expand
Automated exploration of the low-energy chemical space with fast quantum chemical methods.
TLDR
An efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm is proposed and discussed, opening many possible applications in modern computational chemistry and drug discovery. Expand
Toward interactive scanning tunneling microscopy simulations of large-scale molecular systems in real time
We have developed a simulation tool in which structural or chemical modifications of an adsorbed molecular layer can be interactively performed, and where structural relaxation and nearly real-timeExpand
Unsupervised search of low-lying conformers with spectroscopic accuracy: A two-step algorithm rooted into the island model evolutionary algorithm.
TLDR
The performances of different semi-empirical methods for the exploration step and the comparison between stochastic and meta-heuristic algorithms in achieving a cheap yet complete exploration of the conformational space for medium sized chromophores are addressed. Expand
Automated Identification of Relevant Frontier Orbitals for Chemical Compounds and Processes.
TLDR
An automated selection of this active orbital space, that would otherwise be a tedious and error prone manual procedure, is proposed, and this scheme is extended to demonstrate its capability for the selection of consistent active spaces for several excited states and along reaction coordinates. Expand
Reaction prediction via atomistic simulation: from quantum mechanics to machine learning
TLDR
The stochastic surface walking global pathway sampling based on the global neural network (SSW-NN) potential, developed in the group since 2013, is elaborate, which can explore complex reactions systems unbiasedly and automatedly. Expand
Sampling molecular conformations and dynamics in a multiuser virtual reality framework
TLDR
A series of controlled studies quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modeling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically three-dimensional. Expand
...
1
2
3
4
...

References

SHOWING 1-10 OF 111 REFERENCES
Haptic quantum chemistry
TLDR
An implementation designed to physically experience quantum mechanical forces between reactants in chemical reactions by means of a force‐feedback haptic device and a new IMLS‐based method to locate minimum‐energy paths between two points on a potential energy surface is introduced. Expand
Real‐time quantum chemistry
Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be ableExpand
Block‐adaptive quantum mechanics: An adaptive divide‐and‐conquer approach to interactive quantum chemistry
TLDR
This work presents a novel Block‐Adaptive Quantum Mechanics approach to interactive quantum chemistry and demonstrates interactive rates and efficient virtual prototyping for systems containing more than a thousand of atoms on a standard desktop computer. Expand
Interactive physically-based structural modeling of hydrocarbon systems
TLDR
This paper introduces a new adaptive simulation algorithm, as well as a novel algorithm to incrementally update the forces and the total potential energy based on the list of updated relative atomic positions, to enable efficient physically-based editing of hydrocarbon systems. Expand
Theory and applications of computational chemistry : the first forty years
Computing Technologies, Theories, and Algorithms. The Making of 40 Years and More of Theoretical and Computational. A Dynamical, Time-Dependent View of Molecular Theory. Computation of Non-covalentExpand
Taking Ockham's razor to enzyme dynamics and catalysis.
The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kineticExpand
Interactive quantum chemistry: A divide‐and‐conquer ASED‐MO method
We present interactive quantum chemistry simulation at the atom superposition and electron delocalization molecular orbital (ASED‐MO) level of theory. Our method is based on the divide‐and‐conquerExpand
Comparing position and force control for interactive molecular simulators with haptic feedback.
TLDR
This paper presents a novel tool for the analysis of new molecular structures which enables a wide variety of manipulations and for the first time the applications of force control are detailed for molecular simulation. Expand
Haptic representation of the atom
  • Erica Harvey, Chaim Gingold
  • Computer Science
  • 2000 IEEE Conference on Information Visualization. An International Conference on Computer Visualization and Graphics
  • 2000
TLDR
The work tackles the altogether different problem of haptically visualizing the probability density functions of individual atomic orbitals. Expand
Biosynthetic consequences of multiple sequential post-transition-state bifurcations.
TLDR
A system for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations is described, which redefine the challenges faced by nature in controlling the biosynthesis of complex natural products. Expand
...
1
2
3
4
5
...