Predicting Excited-State and Luminescence Properties of a Cyclometalated Iridium(III) Complex: Quantum Mechanics/Molecular Mechanics Study

2021 ◽  
Author(s):  
Yuan-Jun Gao ◽  
Ting-Ting Zhang ◽  
Wen-Kai Chen
Keyword(s):  
Quantum Mechanics ◽  
Excited State ◽  
Molecular Mechanics ◽  
Luminescence Properties

Computational Photobiology and Beyond

2010 ◽  
Vol 63 (3) ◽  
pp. 413 ◽  
Author(s):  
Igor Schapiro ◽  
Mikhail N. Ryazantsev ◽  
Wan Jian Ding ◽  
Mark M. Huntress ◽  
Federico Melaccio ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Excited State ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Chemical Treatment ◽  
Quantum Chemical ◽  
Organic Molecules ◽  
Molecular Devices ◽  
Computational Studies ◽  
Computational Investigation

In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.

On-the-Fly Determination of Active Region Centers in Adaptive-Partitioning QM/MM

2020 ◽  
Author(s):  
Zenghui Yang
Keyword(s):  
Quantum Mechanics ◽  
Active Region ◽  
Molecular Mechanics ◽  
Active Regions ◽  
Available Energy ◽  
Adaptive Partitioning ◽  
Different Levels

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Visualization and Manipulation of Molecular Motion in Solid State through Photo-Induced Clusteroluminescence

2019 ◽  
Author(s):  
Haoke Zhang ◽  
Lili Du ◽  
Lin Wang ◽  
Junkai Liu ◽  
Qing Wan ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Excited State ◽  
Solid State ◽  
Light Source ◽  
Molecular Motion ◽  
Molecular Machine ◽  
Conjugated Molecules ◽  
Time Resolved ◽  
Packing Structure ◽  
New Strategy

<p>Building molecular machine has long been a dream of scientists as it is expected to revolutionize many aspects of technology and medicine. Implementing the solid-state molecular motion is the prerequisite for a practical molecular machine. However, few works on solid-state molecular motion have been reported and it is almost impossible to “see” the motion even if it happens. Here the light-driven molecular motion in solid state is discovered in two non-conjugated molecules <i>s</i>-DPE and <i>s</i>-DPE-TM, resulting in the formation of excited-state though-space complex (ESTSC). Meanwhile, the newly formed ESTSC generates an abnormal visible emission which is termed as clusteroluminescence. Notably, the original packing structure can recover from ESTSC when the light source is removed. These processes have been confirmed by time-resolved spectroscopy and quantum mechanics calculation. This work provides a new strategy to manipulate and “see” solid-state molecular motion and gains new insights into the mechanistic picture of clusteroluminescence.<br></p>

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching

2007 ◽  
Vol 3 (2) ◽  
pp. 628-639 ◽  
Author(s):  
Patrick Maurer ◽  
Alessandro Laio ◽  
Håkan W. Hugosson ◽  
Maria Carola Colombo ◽  
Ursula Rothlisberger
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Force Fields ◽  
Force Matching
Sign in / Sign up

Export Citation Format

Share Document