1
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Rau T, Sedlmair M, Köhn A. chARpack: The Chemistry Augmented Reality Package. J Chem Inf Model 2024. [PMID: 38814047 DOI: 10.1021/acs.jcim.4c00462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Off-loading visualization and interaction into virtual reality (VR) using head-mounted displays (HMDs) has gained considerable popularity in simulation sciences, particularly in chemical modeling. Because of its unique way of soft immersion, augmented reality (AR) HMD technology has even more potential to be integrated into the everyday workflow of computational chemists. In this work, we present our environment to explore the prospects of AR in chemistry and general molecular sciences: The chemistry in Augmented Reality package (chARpack). Besides providing an extensible framework, our software focuses on a seamless transition between a 3D stereoscopic view with true 3D interactions and the traditional desktop PC setup to provide users with the best setup for all tasks in their workflow. Using feedback from domain experts, we discuss our design requirements for this kind of hybrid working environment (AR + PC), regarding input, features, degree of immersion, and collaboration.
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Affiliation(s)
- Tobias Rau
- Institute for Theoretical Chemistry, University of Stuttgart, Stuttgart 70569, Germany
- Institute for Visualization and Interactive Systems, University of Stuttgart, Stuttgart 70569, Germany
| | - Michael Sedlmair
- Institute for Visualization and Interactive Systems, University of Stuttgart, Stuttgart 70569, Germany
| | - Andreas Köhn
- Institute for Theoretical Chemistry, University of Stuttgart, Stuttgart 70569, Germany
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2
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Brown KE, Heise N, Eitel CM, Nelson J, Garbe BA, Meyer CA, Ivie KR, Clapp TR. A Large-Scale, Multiplayer Virtual Reality Deployment: A Novel Approach to Distance Education in Human Anatomy. MEDICAL SCIENCE EDUCATOR 2023; 33:409-421. [PMID: 36820280 PMCID: PMC9933027 DOI: 10.1007/s40670-023-01751-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 05/31/2023]
Abstract
The arrival of COVID-19 restrictions and the increasing demand of online instruction options posed challenges to education communities worldwide, especially in human anatomy. In response, Colorado State University developed and deployed an 8-week-long large-scale virtual reality (VR) course to supplement online human anatomy instruction. Students (n = 75) received a VR-capable laptop and head-mounted display and participated in weekly synchronous group laboratory sessions with instructors. The software enabled students to remotely collaborate in a common virtual space to work with human anatomy using an artist-rendered cadaver. Qualitative data were collected on student engagement, confidence, and reactions to the new technology. Quantitative data assessed student knowledge acquisition and retention of anatomical spatial relationships. Results indicated that students performed better in the online course (mean = 82.27%) when compared to previous in-person laboratories (mean = 80.08%). The utilization of VR promoted student engagement and increased opportunities for student interaction with teaching assistants, peers, and course content. Notably, students reported benefits that focused on unique aspects of their virtual learning environment, including the ability to infinitely scale the cadaver and walk inside and around anatomical structures. Results suggested that using VR was equivalent to 2D methods in student learning and retention of anatomical relationships. Overall, the virtual classroom maintained the rigor of traditional gross anatomy laboratories without negatively impacting student examination scores and provided a high level of accessibility, without compromising learner engagement. Supplementary Information The online version contains supplementary material available at 10.1007/s40670-023-01751-w.
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Affiliation(s)
- Katelyn E. Brown
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO USA
| | - Natascha Heise
- Department of Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA USA
| | - Chad M. Eitel
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO USA
| | - Jordan Nelson
- School of Medicine, University of Colorado Anschutz, Aurora, CO USA
| | | | - Carolyn A. Meyer
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO USA
| | - Kenneth R Ivie
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO USA
| | - Tod R. Clapp
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO USA
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3
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Stella E, Agosti I, Di Blas N, Finazzi M, Lanzi PL, Loiacono D. A virtual reality classroom to teach and explore crystal solid state structures. MULTIMEDIA TOOLS AND APPLICATIONS 2022; 82:6993-7016. [PMID: 35971458 PMCID: PMC9365684 DOI: 10.1007/s11042-022-13410-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 03/01/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED We present an educational application of virtual reality that we created to help students gain an in-depth understanding of the internal structure of crystals and related key concepts. Teachers can use it to give lectures to small groups (10-15) of students in a shared virtual environment, both remotely (with teacher and students in different locations) and locally (while sharing the same physical space). Lectures can be recorded, stored in an online repository, and shared with students who can either review a recorded lecture in the same virtual environment or can use the application for self-studying by exploring a large collection of available crystal structures. We validated our application with human subjects receiving positive feedback. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11042-022-13410-0https://doi.org/10.1007/s11042-022-13410-0.
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4
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Shannon RJ, Deeks HM, Burfoot E, Clark E, Jones AJ, Mulholland AJ, Glowacki DR. Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists. J Chem Phys 2021; 155:154106. [PMID: 34686059 DOI: 10.1063/5.0062517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR "game" was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and "molecular snapshots" from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge.
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Affiliation(s)
- Robin J Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Helen M Deeks
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Eleanor Burfoot
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Edward Clark
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Alex J Jones
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - David R Glowacki
- ArtSci Foundation International, 5th floor Mariner House, Bristol, BS1 4QD, United Kingdom
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5
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Barone V, Puzzarini C, Mancini G. Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy. Phys Chem Chem Phys 2021; 23:17079-17096. [PMID: 34346437 DOI: 10.1039/d1cp02507d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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6
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d'Ischia M, Manini P, Martins Z, Remusat L, O'D Alexander CM, Puzzarini C, Barone V, Saladino R. Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life? Phys Life Rev 2021; 37:65-93. [PMID: 33774429 DOI: 10.1016/j.plrev.2021.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/11/2022]
Abstract
An interdisciplinary review of the chemical literature that points to a unifying scenario for the origin of life, referred to as the Primordial Multifunctional organic Entity (PriME) scenario, is provided herein. In the PriME scenario it is suggested that the Insoluble Organic Matter (IOM) in carbonaceous chondrites, as well as interplanetary dust particles from meteorites and comets may have played an important role in the three most critical processes involved in the origin of life, namely 1) metabolism, via a) the provision and accumulation of molecules that are the building blocks of life, b) catalysis (e.g., by templation), and c) protection of developing life molecules against radiation by excited state deactivation; 2) compartmentalization, via adsorption of compounds on the exposed organic surfaces in fractured meteorites, and 3) replication, via deaggregation, desorption and related physical phenomena. This scenario is based on the hitherto overlooked structural and physicochemical similarities between the IOM and the dark, insoluble, multifunctional melanin polymers found in bacteria and fungi and associated with the ability of these microorganisms to survive extreme conditions, including ionizing radiation. The underlying conceptual link between these two materials is strengthened by the fact that primary precursors of bacterial and fungal melanins (collectively referred to herein as allomelanins) are hydroxylated aromatic compounds like homogentisic acid and 1,8-dihydroxynaphthalene, and that similar hydroxylated aromatic compounds, including hydroxynaphthalenes, figure prominently among possible components of the organic materials on dust grains and ices in the interstellar matter, and may be involved in the formation of IOM in meteorites. Inspired by this rationale, a vis-à-vis review of the properties of IOM from various chondrites and non-nitrogenous allomelanin pigments from bacteria and fungi is provided herein. The unrecognized similarities between these materials may pave the way for a novel scenario at the origin of life, in which IOM-related complex organic polymers delivered to the early Earth are proposed to serve as PriME and were preserved and transformed in those primitive forms of life that shared the ability to synthesize melanin polymers playing an important role in the critical processes underlying the establishment of terrestrial eukaryotes.
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Affiliation(s)
- Marco d'Ischia
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy.
| | - Paola Manini
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Zita Martins
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Laurent Remusat
- Institut de minéralogie, de physique des matériaux et de cosmochimie, UMR CNRS 7590, Sorbonne Université, Muséum National d'Histoire Naturelle, 61 rue Buffon, 75005 Paris, France
| | - Conel M O'D Alexander
- Earth and Planets Laboratory, Carnegie Institution for Science, 5241 Broad Branch Road, NW Washington, DC 20015-1305, USA
| | - Cristina Puzzarini
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via F. Selmi 2, Bologna, I-40126, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, I-56126, Italy
| | - Raffaele Saladino
- Biological and Ecological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis 01100 Viterbo, Italy
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7
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Juárez-Jiménez J, Tew P, O Connor M, Llabrés S, Sage R, Glowacki D, Michel J. Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes. J Chem Inf Model 2020; 60:6344-6354. [PMID: 33180485 DOI: 10.1021/acs.jcim.0c00221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Molecular dynamics (MD) simulations are increasingly used to elucidate relationships between protein structure, dynamics, and their biological function. Currently, it is extremely challenging to perform MD simulations of large-scale structural rearrangements in proteins that occur on millisecond timescales or beyond, as this requires very significant computational resources, or the use of cumbersome "collective variable" enhanced sampling protocols. Here, we describe a framework that combines ensemble MD simulations and virtual reality visualization (eMD-VR) to enable users to interactively generate realistic descriptions of large amplitude, millisecond timescale protein conformational changes in proteins. Detailed tests demonstrate that eMD-VR substantially decreases the computational cost of folding simulations of a WW domain, without the need to define collective variables a priori. We further show that eMD-VR generated pathways can be combined with Markov state models to describe the thermodynamics and kinetics of large-scale loop motions in the enzyme cyclophilin A. Our results suggest eMD-VR is a powerful tool for exploring protein energy landscapes in bioengineering efforts.
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Affiliation(s)
- Jordi Juárez-Jiménez
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Philip Tew
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, United Kingdom
| | - Michael O Connor
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.,Department of Computer Science, University of Bristol, Merchant Venture's Building, Bristol BS8 1UB, United Kingdom.,Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Salomé Llabrés
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Rebecca Sage
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, United Kingdom
| | - David Glowacki
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.,Department of Computer Science, University of Bristol, Merchant Venture's Building, Bristol BS8 1UB, United Kingdom.,Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Julien Michel
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
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8
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Barone V, Puzzarini C. Looking for the bricks of the life in the interstellar medium: The fascinating world of astrochemistry. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202024600021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The discovery in the interstellar medium of molecules showing a certain degree of complexity, and in particular those with a prebiotic character, has attracted great interest. A complex chemistry takes place in space, but the processes that lead to the production of molecular species are a matter of intense discussion, the knowledge still being at a rather primitive stage. Debate on the origins of interstellar molecules has been further stimulated by the identification of biomolecular building blocks, such as nucleobases and amino acids, in meteorites and comets. Since many of the molecules found in space play a role in the chemistry of life, the issue of their molecular genesis and evolution might be related to the profound question of the origin of life itself. Understanding the underlying chemical processes, including the production, reactions and destruction of compounds, requires the concomitant study of spectroscopy, gas-phase reactivity, and heterogeneous processes on dust-grains. The aim of this contribution is to provide a general view of a complex and multifaceted challenge, while focusing on the role played by molecular spectroscopy and quantum-chemical computations. In particular, the derivation of the molecular spectroscopic features and the investigation of gas-phase formation routes of prebiotic species in the interstellar medium are addressed from a computational point of view.
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9
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Mancini G, Fusè M, Lazzari F, Chandramouli B, Barone V. Unsupervised search of low-lying conformers with spectroscopic accuracy: A two-step algorithm rooted into the island model evolutionary algorithm. J Chem Phys 2020; 153:124110. [DOI: 10.1063/5.0018314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Federico Lazzari
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | | | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
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10
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Calvelo M, Piñeiro Á, Garcia-Fandino R. An immersive journey to the molecular structure of SARS-CoV-2: Virtual reality in COVID-19. Comput Struct Biotechnol J 2020; 18:2621-2628. [PMID: 32983399 PMCID: PMC7500438 DOI: 10.1016/j.csbj.2020.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 02/04/2023] Open
Abstract
The era of the explosion of immersive technologies has bumped head-on with the coronavirus disease 2019 (COVID-19) global pandemic caused by the severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2). The proper understanding of the three-dimensional structures that compose the virus, as well as of those involved in the infection process and in treatments, is expected to contribute to the advance of fundamental and applied research against this pandemic, including basic molecular biology studies and drug design. Virtual reality (VR) is a powerful technology to visualize the biomolecular structures that are currently being identified for SARS-CoV-2 infection, opening possibilities to significant advances in the understanding of the disease-associate mechanisms and thus to boost new therapies and treatments. The present availability of VR for a large variety of practical applications together with the increasingly easiness, quality and economic access of this technology is transforming the way we interact with digital information. Here, we review the software implementations currently available for VR visualization of SARS-CoV-2 molecular structures, covering a range of virtual environments: CAVEs, desktop software, and cell phone applications, all of them combined with head-mounted devices like cardboards, Oculus Rift or the HTC Vive. We aim to impulse and facilitate the use of these emerging technologies in research against COVID-19 trying to increase the knowledge and thus minimizing risks before placing huge amounts of money for the development of potential treatments.
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Affiliation(s)
- Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain.,Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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11
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Del Galdo S, Fusè M, Barone V. CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach. Front Chem 2020; 8:584. [PMID: 32733856 PMCID: PMC7358700 DOI: 10.3389/fchem.2020.00584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/05/2020] [Indexed: 11/16/2022] Open
Abstract
We extend a recently proposed computational strategy for the simulation of absorption spectra of semi-rigid molecular systems in condensed phases to the emission spectra of flexible chromophores. As a case study, we have chosen the CPL spectrum of camphor in methanol solution, which shows a well-defined bisignate shape. The first step of our approach is the quantum mechanical computation of reference spectra including vibrational averaging effects and taking bulk solvent effects into account by means of the polarizable continuum model. In the present case, the large amplitude inversion mode is explicitly treated by a numerical approach, whereas the other small-amplitude vibrational modes are taken into account within the harmonic approximation. Next, the snapshots of classical molecular dynamics computations are clusterized and one representative configuration from each cluster is used to compute a reference spectrum. In the present case, different clusters correspond to the two stable conformers of camphor in the S1 excited electronic state and, for each of them, to different numbers of strong solute-solvent hydrogen bonds. Finally, local fluctuation effects within each cluster are taken into account by means of the perturbed matrix model. The overall procedure leads to good agreement with experiment for absorption and emission spectra together with their chiral counterparts, thus allowing to analyze the role of different effects (stereo-electronic, vibrational, environmental) in tuning the overall experimental spectra.
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Affiliation(s)
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore, Pisa, Italy
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12
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Lazzari F, Salvadori A, Mancini G, Barone V. Molecular Perception for Visualization and Computation: The Proxima Library. J Chem Inf Model 2020; 60:2668-2672. [PMID: 32271572 PMCID: PMC7997373 DOI: 10.1021/acs.jcim.0c00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proxima is a molecular perception library designed with a double purpose: to be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies. The current version of Proxima is available for evaluation purposes at https://bitbucket.org/sns-smartlab/proxima/src/master/.
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Affiliation(s)
- Federico Lazzari
- Scuola Normale Superiore, Piazza dei Cavalieri, 7-56126 Pisa, Italy
| | - Andrea Salvadori
- Scuola Normale Superiore, Piazza dei Cavalieri, 7-56126 Pisa, Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri, 7-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri, 7-56126 Pisa, Italy
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13
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A never-ending story in the sky: The secrets of chemical evolution. Phys Life Rev 2020; 32:59-94. [DOI: 10.1016/j.plrev.2019.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 01/13/2023]
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14
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Doak DG, Denyer GS, Gerrard JA, Mackay JP, Allison JR. Peppy: A virtual reality environment for exploring the principles of polypeptide structure. Protein Sci 2019; 29:157-168. [PMID: 31622516 DOI: 10.1002/pro.3752] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 11/06/2022]
Abstract
A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two-dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research-oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are strengths in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone φ/ψ angles, basic chemical structure, and steric effects on a polypeptide structure in an accessible format that is novel, dynamic, and fun to use. Apart from describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses.
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Affiliation(s)
- David G Doak
- Games Art and Design, Norwich University of the Arts, Norwich, UK
| | - Gareth S Denyer
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Juliet A Gerrard
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Jane R Allison
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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15
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Jiménez ZA. Teaching and Learning Chemistry via Augmented and Immersive Virtual Reality. ACTA ACUST UNITED AC 2019. [DOI: 10.1021/bk-2019-1318.ch003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Affiliation(s)
- Zulma A. Jiménez
- Notre Dame of Maryland University, 4701 North Charles Street, Baltimore, Maryland 21210, United States
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16
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O'Connor MB, Bennie SJ, Deeks HM, Jamieson-Binnie A, Jones AJ, Shannon RJ, Walters R, Mitchell TJ, Mulholland AJ, Glowacki DR. Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework. J Chem Phys 2019; 150:220901. [PMID: 31202243 DOI: 10.1063/1.5092590] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.
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Affiliation(s)
- Michael B O'Connor
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Simon J Bennie
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Helen M Deeks
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Alexander Jamieson-Binnie
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Alex J Jones
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Robin J Shannon
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Rebecca Walters
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Thomas J Mitchell
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - David R Glowacki
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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17
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Puzzarini C, Bloino J, Tasinato N, Barone V. Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy. Chem Rev 2019; 119:8131-8191. [DOI: 10.1021/acs.chemrev.9b00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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18
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Kingsley LJ, Brunet V, Lelais G, McCloskey S, Milliken K, Leija E, Fuhs SR, Wang K, Zhou E, Spraggon G. Development of a virtual reality platform for effective communication of structural data in drug discovery. J Mol Graph Model 2019; 89:234-241. [DOI: 10.1016/j.jmgm.2019.03.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 10/27/2022]
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19
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Fusè M, Egidi F, Bloino J. Vibrational circular dichroism under the quantum magnifying glass: from the electronic flow to the spectroscopic observable. Phys Chem Chem Phys 2019; 21:4224-4239. [DOI: 10.1039/c8cp06514d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A chemically intuitive method to analyse and interpret vibrational circular dichroism spectra based on the vibrational transition current density.
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Affiliation(s)
- Marco Fusè
- Scuola Normale Superiore
- Piazza dei Cavalieri 7
- Pisa
- Italy
| | - Franco Egidi
- Scuola Normale Superiore
- Piazza dei Cavalieri 7
- Pisa
- Italy
| | - Julien Bloino
- Scuola Normale Superiore
- Piazza dei Cavalieri 7
- Pisa
- Italy
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20
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Simm GN, Vaucher AC, Reiher M. Exploration of Reaction Pathways and Chemical Transformation Networks. J Phys Chem A 2018; 123:385-399. [DOI: 10.1021/acs.jpca.8b10007] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gregor N. Simm
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Alain C. Vaucher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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21
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Salvadori A, Fusè M, Mancini G, Rampino S, Barone V. Diving into chemical bonding: An immersive analysis of the electron charge rearrangement through virtual reality. J Comput Chem 2018; 39:2607-2617. [DOI: 10.1002/jcc.25523] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Andrea Salvadori
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
| | - Marco Fusè
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
| | - Giordano Mancini
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
| | - Sergio Rampino
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
| | - Vincenzo Barone
- SMART Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri 7; 56126 Pisa Italy
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22
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Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. Molecular Visualization on the Holodeck. J Mol Biol 2018; 430:3982-3996. [PMID: 29964044 DOI: 10.1016/j.jmb.2018.06.040] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/15/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
Abstract
Can virtual reality be useful for visualizing and analyzing molecular structures and three-dimensional (3D) microscopy? Uses we are exploring include studies of drug binding to proteins and the effects of mutations, building accurate atomic models in electron microscopy and x-ray density maps, understanding how immune system cells move using 3D light microscopy, and teaching schoolchildren about biomolecules that are the machinery of life. Virtual reality (VR) offers immersive display with a wide field of view and head tracking for better perception of molecular architectures and uses 6-degree-of-freedom hand controllers for simple manipulation of 3D data. Conventional computer displays with trackpad, mouse and keyboard excel at two-dimensional tasks such as writing and studying research literature, uses for which VR technology is at present far inferior. Adding VR to the conventional computing environment could improve 3D capabilities if new user-interface problems can be solved. We have developed three VR applications: ChimeraX for analyzing molecular structures and electron and light microscopy data, AltPDB for collaborative discussions around atomic models, and Molecular Zoo for teaching young students characteristics of biomolecules. Investigations over three decades have produced an extensive literature evaluating the potential of VR in research and education. Consumer VR headsets are now affordable to researchers and educators, allowing direct tests of whether the technology is valuable in these areas. We survey here advantages and disadvantages of VR for molecular biology in the context of affordable and dramatically more powerful VR and graphics hardware than has been available in the past.
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Affiliation(s)
- Thomas D Goddard
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Alan A Brilliant
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | | | | | - James Tyrwhitt-Drake
- Bioinformatics and Computational Biosciences Branch, NIH National Institute of Allergy and Infectious Disease, Rockville, MD 20852, USA
| | - Elaine C Meng
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
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23
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Wiebrands M, Malajczuk CJ, Woods AJ, Rohl AL, Mancera RL. Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2018-0010/jib-2018-0010.xml. [PMID: 29927749 PMCID: PMC6167041 DOI: 10.1515/jib-2018-0010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/09/2018] [Indexed: 11/15/2022] Open
Abstract
Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.
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Affiliation(s)
- Michael Wiebrands
- Curtin Hub for Immersive Visualization and eResearch (HIVE), Curtin University, Perth, WA, Australia
| | - Chris J Malajczuk
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Centre and Curtin Institute for Computation, Curtin University, Perth, WA, Australia
| | - Andrew J Woods
- Curtin Hub for Immersive Visualization and eResearch (HIVE), Curtin University, Perth, WA, Australia
| | - Andrew L Rohl
- School of Molecular and Life Sciences and Curtin Institute for Computation, Curtin University, Perth WA, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Centre and Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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24
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Müller C, Krone M, Huber M, Biener V, Herr D, Koch S, Reina G, Weiskopf D, Ertl T. Interactive Molecular Graphics for Augmented Reality Using HoloLens. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2018-0005/jib-2018-0005.xml. [PMID: 29897886 PMCID: PMC6167047 DOI: 10.1515/jib-2018-0005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/09/2018] [Indexed: 11/18/2022] Open
Abstract
Immersive technologies like stereo rendering, virtual reality, or augmented reality (AR) are often used in the field of molecular visualisation. Modern, comparably lightweight and affordable AR headsets like Microsoft’s HoloLens open up new possibilities for immersive analytics in molecular visualisation. A crucial factor for a comprehensive analysis of molecular data in AR is the rendering speed. HoloLens, however, has limited hardware capabilities due to requirements like battery life, fanless cooling and weight. Consequently, insights from best practises for powerful desktop hardware may not be transferable. Therefore, we evaluate the capabilities of the HoloLens hardware for modern, GPU-enabled, high-quality rendering methods for the space-filling model commonly used in molecular visualisation. We also assess the scalability for large molecular data sets. Based on the results, we discuss ideas and possibilities for immersive molecular analytics. Besides more obvious benefits like the stereoscopic rendering offered by the device, this specifically includes natural user interfaces that use physical navigation instead of the traditional virtual one. Furthermore, we consider different scenarios for such an immersive system, ranging from educational use to collaborative scenarios.
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Affiliation(s)
- Christoph Müller
- Visualisation Research Centre (VISUS), University of Stuttgart, 70569 Stuttgart, Germany
| | - Michael Krone
- Visualisation Research Centre (VISUS), University of Stuttgart, 70569 Stuttgart, Germany
| | - Markus Huber
- Visualisation Research Centre (VISUS), University of Stuttgart, 70569 Stuttgart, Germany
| | - Verena Biener
- Visualisation Research Centre (VISUS), University of Stuttgart, 70569 Stuttgart, Germany
| | - Dominik Herr
- Institute for Visualisation and Interactive Systems (VIS), University of Stuttgart, 70569 Stuttgart, Germany.,Graduate School Advanced Manufacturing Engineering (GSaME), University of Stuttgart, 70569 Stuttgart, Germany
| | - Steffen Koch
- Institute for Visualisation and Interactive Systems (VIS), University of Stuttgart, 70569 Stuttgart, Germany
| | - Guido Reina
- Visualisation Research Centre (VISUS), University of Stuttgart, 70569 Stuttgart, Germany
| | - Daniel Weiskopf
- Visualisation Research Centre (VISUS), University of Stuttgart, 70569 Stuttgart, Germany.,Institute for Visualisation and Interactive Systems (VIS), University of Stuttgart, 70569 Stuttgart, Germany
| | - Thomas Ertl
- Visualisation Research Centre (VISUS), University of Stuttgart, 70569 Stuttgart, Germany.,Institute for Visualisation and Interactive Systems (VIS), University of Stuttgart, 70569 Stuttgart, Germany
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25
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Egidi F, Fusè M, Baiardi A, Bloino J, Li X, Barone V. Computational simulation of vibrationally resolved spectra for spin-forbidden transitions. Chirality 2018; 30:850-865. [PMID: 29727500 DOI: 10.1002/chir.22864] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/25/2022]
Abstract
In this computational study, we illustrate a method for computing phosphorescence and circularly polarized phosphorescence spectra of molecular systems, which takes into account vibronic effects including both Franck-Condon and Herzberg-Teller contributions. The singlet and triplet states involved in the phosphorescent emission are described within the harmonic approximation, and the method fully takes mode-mixing effects into account when evaluating Franck-Condon integrals. Spin-orbit couplings, which are responsible for these otherwise forbidden phenomena, are accounted for by means of a relativistic two-component time-dependent density functional theory method. The model is applied to two types of chiral systems: camphorquinone, a rigid organic system that allows for an extensive benchmark, and some members of a class of iridium complexes. The merits and shortcomings of the methods are discussed, and some perspectives for future developments are offered.
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Affiliation(s)
| | | | | | - Julien Bloino
- Institute of Chemistry of Organometallic Compounds, National Research Council of Italy, Pisa, Italy
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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26
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Aspuru-Guzik A, Lindh R, Reiher M. The Matter Simulation (R)evolution. ACS CENTRAL SCIENCE 2018; 4:144-152. [PMID: 29532014 PMCID: PMC5832995 DOI: 10.1021/acscentsci.7b00550] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 05/26/2023]
Abstract
To date, the program for the development of methods and models for atomistic and continuum simulation directed toward chemicals and materials has reached an incredible degree of sophistication and maturity. Currently, one can witness an increasingly rapid emergence of advances in computing, artificial intelligence, and robotics. This drives us to consider the future of computer simulation of matter from the molecular to the human length and time scales in a radical way that deliberately dares to go beyond the foreseeable next steps in any given discipline. This perspective article presents a view on this future development that we believe is likely to become a reality during our lifetime.
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Affiliation(s)
- Alán Aspuru-Guzik
- Department of Chemistry
and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Canadian Institute for Advanced Research
(CIFAR), Toronto, Ontario M5G 1Z8, Canada
| | - Roland Lindh
- Department of Chemistry−Ångström,
The Theoretical Chemistry Programme, and Uppsala Center for Computational
Chemistry—UC3, Uppsala University, Box 518, 751 20 Uppsala, Sweden
| | - Markus Reiher
- Laboratory of Physical
Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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27
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Macchiagodena M, Mancini G, Pagliai M, Del Frate G, Barone V. Fine-tuning of atomic point charges: Classical simulations of pyridine in different environments. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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ChemPreview : an augmented reality-based molecular interface. J Mol Graph Model 2017; 73:18-23. [DOI: 10.1016/j.jmgm.2017.01.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/26/2017] [Accepted: 01/27/2017] [Indexed: 11/19/2022]
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29
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Fusè M, Rimoldi I, Cesarotti E, Rampino S, Barone V. On the relation between carbonyl stretching frequencies and the donor power of chelating diphosphines in nickel dicarbonyl complexes. Phys Chem Chem Phys 2017; 19:9028-9038. [PMID: 28304027 PMCID: PMC5436090 DOI: 10.1039/c7cp00982h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/05/2017] [Indexed: 11/24/2022]
Abstract
The relation between spectroscopic observables and the detailed metal-ligand bonding features in chelation complexes is addressed using both experimental and state-of-the-art theoretical and computational methods. We synthesized and characterized a set of six nickel dicarbonyl complexes of general formula [Ni(CO)2(PP)], where PP is an atropoisomeric chelating diphosphine ligand. The analysis of the obtained experimental data and the basicity and oxidative potentials of the free ligands suggests a close relation between the donor ability of the chelating ligand and the carbonyl stretching frequencies observed in the complexes. We then use theory to unravel the detailed mechanisms of chelation-bond formation in terms of partial charge flows between the molecular orbitals of the fragments. By extending the promising, recently published natural orbitals for chemical valence/charge displacement (NOCV/CD) analysis scheme we provide a thorough, quantitative description of the several charge fluxes following the metal-ligand bond formation and demonstrate that the carbonyl stretching frequencies in the considered complexes selectively respond to the σ-donation charge flow from the phosphorus lone pairs of the ligands, with the frequency shift being in quantitative correlation with the extent of the ligand-to-metal charge transfer.
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Affiliation(s)
- Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Isabella Rimoldi
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Edoardo Cesarotti
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Sergio Rampino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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30
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Vaucher AC, Reiher M. Steering Orbital Optimization out of Local Minima and Saddle Points Toward Lower Energy. J Chem Theory Comput 2017; 13:1219-1228. [DOI: 10.1021/acs.jctc.7b00011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alain C. Vaucher
- Laboratorium für Physikalische
Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische
Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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