1
|
Nottoli G, Ballotta B, Rampino S. Local Charge-Displacement Analysis: Targeting Local Charge-Flows in Complex Intermolecular Interactions. J Chem Phys 2022; 157:084107. [DOI: 10.1063/5.0095142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Charge-displacement (CD) analysis has recently proven to be a simple and powerful scheme for quantitatively analyzing the profile of the charge redistribution occurring upon intermolecular interactions along a given interaction axis. However, when two molecular fragments bind through complex interactions involving multiple concurrent charge flows, ordinary CD analysis is capable of providing only an averaged picture of the related charge-flow profiles and no detailed information on each of them. In this article, we combine CD analysis with a Hirshfeld partitioning of the molecular charge redistribution for a local analysis on focused portions of the molecule, allowing for a detailed characterization of one charge flow at a time. The resulting scheme - the local charge-displacement (LCD) analysis - is tested on the intriguing case of the dimethyl sulfide (DMS)-sulfur dioxide (SO2) complex, characterized by concurrent charge flows relating to a sulfur-sulfur homo-chalcogen interaction and a pair of hydrogen bonds. The LCD scheme is then applied to the analysis of multiple hydrogen bonding in the acetic acid dimer, of base-pairing interactions in DNA, and of ambifunctional hydrogen bonding in the ammonia-pyridine complex.
Collapse
|
2
|
Lanrezac A, Férey N, Baaden M. Wielding the power of interactive molecular simulations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- André Lanrezac
- CNRS, Laboratoire de Biochimie Théorique Université de Paris Paris France
| | - Nicolas Férey
- CNRS, Laboratoire interdisciplinaire des sciences du numérique Université Paris‐Saclay Orsay France
| | - Marc Baaden
- CNRS, Laboratoire de Biochimie Théorique Université de Paris Paris France
| |
Collapse
|
3
|
Sagresti L, Rampino S. Charge-Flow Profiles along Curvilinear Paths: A Flexible Scheme for the Analysis of Charge Displacement upon Intermolecular Interactions. Molecules 2021; 26:molecules26216409. [PMID: 34770822 PMCID: PMC8586930 DOI: 10.3390/molecules26216409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/26/2022] Open
Abstract
The Charge-Displacement (CD) analysis has proven to be a powerful tool for a quantitative characterization of the electron-density flow occurring upon chemical bonding along a suitably chosen interaction axis. In several classes of interesting intermolecular interactions, however, an interaction axis cannot be straightforwardly defined, and the CD analysis loses consistency and usefulness. In this article, we propose a general, flexible reformulation of the CD analysis capable of providing a quantitative view of the charge displacement along custom curvilinear paths. The new scheme naturally reduces to ordinary CD analysis if the path is chosen to be a straight line. An implementation based on a discrete sampling of the electron densities and a Voronoi space partitioning is described and shown in action on two test cases of a metal-carbonyl and a pyridine-ammonia complex.
Collapse
Affiliation(s)
- Luca Sagresti
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy;
- Istituto Nazionale di Fisica Nucleare (INFN)—Sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Sergio Rampino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy;
- Istituto Nazionale di Fisica Nucleare (INFN)—Sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
- Correspondence:
| |
Collapse
|
4
|
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.
Collapse
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | | | | |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Ciancaleoni G, Belpassi L. Disentanglement of orthogonal hydrogen and halogen bonds via natural orbital for chemical valence: A charge displacement analysis. J Comput Chem 2020; 41:1185-1193. [PMID: 32011001 DOI: 10.1002/jcc.26165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 01/01/2023]
Abstract
As known, the electron density of covalently bound halogen atoms is anisotropically distributed, making them potentially able to establish many weak interactions, acting at the same time as halogen bond donors and hydrogen bond acceptors. Indeed, there are many examples in which the halogen and hydrogen bond coexist in the same structure and, if a correct bond analysis is required, their separation is mandatory. Here, the advantages and limitations of coupling the charge displacement analysis with natural orbital for chemical valence method (NOCV-CD) to separately analyze orthogonal weak interactions are shown, for both symmetric and asymmetric adducts. The methodology gives optimal results with intermolecular adducts but, in the presence of an organometallic complex, also intramolecular interactions can be correctly analyzed. Beyond the methodological aspects, it is shown that correctly separate and quantify the interactions can give interesting chemical insights about the systems.
Collapse
Affiliation(s)
- Gianluca Ciancaleoni
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, Pisa, Italy
| | - Leonardo Belpassi
- Istituto di Scienze e Tecnologie Chimiche "G. Natta"-CNR (CNR-SCITEC), c/o Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| |
Collapse
|
7
|
A General User-Friendly Tool for Kinetic Calculations of Multi-Step Reactions within the Virtual Multifrequency Spectrometer Project. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10051872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We discuss the implementation of a computer program for accurate calculation of the kinetics of chemical reactions integrated in the user-friendly, multi-purpose Virtual Multifrequency Spectrometer tool. The program is based on the ab initio modeling of the involved molecular species, the adoption of transition-state theory for each elementary step of the reaction, and the use of a master-equation approach accounting for the complete reaction scheme. Some features of the software are illustrated through examples including the interconversion reaction of hydroxyacetone and 2-hydroxypropanal and the production of HCN and HNC from vinyl cyanide.
Collapse
|
8
|
Martino M, Salvadori A, Lazzari F, Paoloni L, Nandi S, Mancini G, Barone V, Rampino S. Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality. J Comput Chem 2020; 41:1310-1323. [PMID: 32058615 DOI: 10.1002/jcc.26172] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/16/2020] [Accepted: 02/03/2020] [Indexed: 01/28/2023]
Abstract
The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.
Collapse
Affiliation(s)
- Marta Martino
- SMART Laboratory, Scuola Normale Superiore, Pisa, Italy
| | | | | | | | - Surajit Nandi
- SMART Laboratory, Scuola Normale Superiore, Pisa, Italy
| | | | | | | |
Collapse
|
9
|
Rossi-Fernández AC, Villegas-Escobar N, Guzmán-Angel D, Gutiérrez-Oliva S, Ferullo RM, Castellani NJ, Toro-Labbé A. Theoretical study of glycine amino acid adsorption on graphene oxide. J Mol Model 2020; 26:33. [PMID: 31982975 DOI: 10.1007/s00894-020-4297-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 01/14/2020] [Indexed: 11/24/2022]
Abstract
The non-dissociative and dissociative adsorptions of zwitterionic Gly on graphene oxide (GO) was studied in the framework of DFT using a cluster model approach. In this work, the interaction with an epoxy group of GO basal plane was mainly considered. As a comparison, the non-dissociative and dissociative adsorptions of neutral Gly were also taken into account. The non-dissociative adsorption modes for zwitterionic and neutral Gly conformers show binding energies of 12.2 and 14.4 kcal mol-1, respectively. These molecules are thought to remain over the GO surface due to attractive noncovalent interactions. Two dissociative adsorption modes, for Z-Gly and N-Gly, show smaller binding energies of 7.2 and 8.4 kcal mol-1, where the deprotonated species links strongly through a C-O or C-N covalent bond to the GO surface. The results obtained in the present theoretical approach to the glycine/graphene oxide system support the fact that glycine can be attached to epoxy groups of graphene oxide basal planes in addition to the anchoring on edge oxidation groups. In summary, we conclude that glycine can be used as a reducing agent as well as a functionalizer of GO sheets.
Collapse
Affiliation(s)
- Ana C Rossi-Fernández
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile. .,Instituto de Química del Sur (INQUISUR), CONICET-UNS, Universidad Nacional del Sur, Av. Alem 1253, 8000, Bahía Blanca, Argentina.
| | - Nery Villegas-Escobar
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Daniela Guzmán-Angel
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Soledad Gutiérrez-Oliva
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Ricardo M Ferullo
- Instituto de Química del Sur (INQUISUR), CONICET-UNS, Universidad Nacional del Sur, Av. Alem 1253, 8000, Bahía Blanca, Argentina
| | - Norberto J Castellani
- Instituto de Física del Sur (IFISUR), CONICET-UNS, Universidad Nacional del Sur, Av. Alem 1253, 8000, Bahía Blanca, Argentina
| | - Alejandro Toro-Labbé
- Departamento de Química-Física, Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| |
Collapse
|
10
|
Potenti S, Paoloni L, Nandi S, Fusè M, Barone V, Rampino S. Chemical bonding in cuprous complexes with simple nitriles: octet rule and resonance concepts versus quantitative charge-redistribution analysis. Phys Chem Chem Phys 2020; 22:20238-20247. [DOI: 10.1039/d0cp01536a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Resonance structures for six cuprous complexes with simple nitriles are interpreted by means of a quantitative analysis of charge redistribution upon copper-nitrile bonding.
Collapse
Affiliation(s)
| | | | - Surajit Nandi
- Scuola Normale Superiore
- SMART Laboratory
- 56126 Pisa
- Italy
| | - Marco Fusè
- Scuola Normale Superiore
- SMART Laboratory
- 56126 Pisa
- Italy
| | - Vincenzo Barone
- Scuola Normale Superiore
- SMART Laboratory
- 56126 Pisa
- Italy
- Istituto Nazionale di Fisica Nucleare (INFN) – Sezione di Pisa
| | - Sergio Rampino
- Scuola Normale Superiore
- SMART Laboratory
- 56126 Pisa
- Italy
- Istituto Nazionale di Fisica Nucleare (INFN) – Sezione di Pisa
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Buttarazzi E, Rosi F, Ciancaleoni G. Influence of halogen bonding on gold(i)-ligand bond components and DFT characterization of a gold-iodine halogen bond. Phys Chem Chem Phys 2019; 21:20478-20485. [PMID: 31463502 DOI: 10.1039/c9cp03811f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A gold(i) complex bearing nitrogen acyclic carbene (NAC) and selenourea (SeU) has been used to verify whether the second-sphere SeI halogen bond (XB) is able to modify the Dewar-Chatt-Duncanson components of the Au-C and Au-Se bonds. The chosen system was found to be thermically unstable but it allowed an in-depth theoretical study by means of Energy Decomposition Analysis, Natural Bond Orbital and Natural Orbitals for Chemical Valence methods, coupled with Charge Displacement analysis. Indeed, in the presence of iodoperfluoroalkanes as XB donors, iodine interacts with the lone pair of the coordinated selenium, enhancing the Au ← C σ donation and depressing the Au → C π back-donation, as demonstrated also by the increase of the rotational barrier of the C-N bond of the NAC (see G. Ciancaleoni and others, Chem. - Eur. J., 2015, 21, 2467). On the other hand, in the presence of N-iodosuccinimide (NIS), the gold directly establishes a XB with the iodine by using its d lone pairs. This AuI XB is favored by the low steric hindrance of the ligands coordinated to the gold and the presence of the amino protons of SeU, which establish additional hydrogen bonds with the NIS. Also in this case, the effect is to increase the σ acidity and decrease the π basicity of the metal.
Collapse
Affiliation(s)
- Edoardo Buttarazzi
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, via Giuseppe Moruzzi 13, Pisa 56124, Italy.
| | | | | |
Collapse
|
13
|
A Modern-Fortran Program for Chemical Kinetics on Top of Anharmonic Vibrational Calculations. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-3-030-24311-1_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
|
14
|
|
15
|
Paoloni L, Rampino S, Barone V. Potential-Energy Surfaces for Ring-Puckering Motions of Flexible Cyclic Molecules through Cremer-Pople Coordinates: Computation, Analysis, and Fitting. J Chem Theory Comput 2019; 15:4280-4294. [PMID: 31244128 DOI: 10.1021/acs.jctc.9b00363] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ring-puckering motion in 12 flexible cyclic molecules is investigated by calculation and analysis of two-dimensional potential-energy surfaces (PESs) using the so-called ring-puckering coordinates proposed by Cremer and Pople. The PESs are calculated by means of density-functional theory using a B2PLYP-D3BJ exchange-correlation functional with a maug-cc-pVTZ basis set, and results are compared to the available experimental and theoretical data. Special care is devoted to the aspect of symmetry in such two-dimensional PESs, which are here reported for the first time also for molecules whose planar form has symmetry lower than D5 h or C2 v. The issue of PES fitting and that of solving the nuclear dynamics using ring-puckering coordinates are also addressed. Analytical formulations of the computed PESs using suitable functional forms with a limited set of parameters are provided.
Collapse
Affiliation(s)
- Lorenzo Paoloni
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| | - Sergio Rampino
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| | - Vincenzo Barone
- SMART Laboratory , Scuola Normale Superiore , Piazza dei Cavalieri 7 , 56126 Pisa , Italia
| |
Collapse
|
16
|
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
| |
Collapse
|
17
|
Hagita K, Matsumoto S, Ota K. Study of Commodity VR for Computational Material Sciences. ACS OMEGA 2019; 4:3990-3999. [PMID: 31459608 PMCID: PMC6649102 DOI: 10.1021/acsomega.8b03483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/25/2019] [Indexed: 06/10/2023]
Abstract
Recent advancements in virtual reality (VR) devices and software environments make it possible to easily incorporate this technology for many applications, including computational materials science. For studying three-dimensional (3D) structure models and related chemical information, we focused on using a commodity VR device (VIVE) and an authoring tool (Unity). To visualize 3D chemical structures, disturbances like judder due to dropped frames should be eliminated from the VR experience to improve simulations. We propose a simple evaluation method that is straightforward for the nonexpert or novice VR user. We examine the major visualization representations including ball, ball and stick, and isosurface systems. For systematic benchmark measurements, a pendulum from the VR device was used to generate periodic oscillatory motion during measurements of a time series in frames per second (fps). For VIVE with a refresh rate of 90 Hz, judder occurred when less than 90 fps. We demonstrated the system size limitations for the results of molecular dynamics simulations of phase separation of ABA block copolymers and experimental observations of filler morphologies in rubber.
Collapse
Affiliation(s)
- Katsumi Hagita
- Department
of Applied Physics, National Defense Academy, 1-10-20 Hashirimizu, Yokosuka 239-8686, Japan
| | - Shigenori Matsumoto
- Research
& Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034, Japan
| | - Koji Ota
- Advanced
Technology Research & Development Center, Hitachi Chemical Co. Ltd., 48 Wadai, Tsukuba, Ibaraki 300-4247, Japan
| |
Collapse
|
18
|
Marrazzini G, Gabbiani C, Ciancaleoni G. Interplay between Gold(I)-Ligand Bond Components and Hydrogen Bonding: A Combined Experimental/Computational Study. ACS OMEGA 2019; 4:1344-1353. [PMID: 31459403 PMCID: PMC6647975 DOI: 10.1021/acsomega.8b03330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/03/2019] [Indexed: 06/10/2023]
Abstract
The influence of weak interactions on the donation/back-donation bond components in the complex [(NHC)Au(SeU)]+ (NHC = N-heterocyclic carbene; SeU = selenourea) has been studied by coupling experimental and theoretical techniques. In particular, NMR 1H and pulsed-field gradient spin-echo titrations allowed us to characterize the hydrogen bond (HB) between the -NH2 moieties of SeU and the anions PF6 - and ClO4 -, whereas 77Se NMR spectroscopy allowed us to characterize the Au-Se bond. Theoretically, the Au-Se and Au-C orbital interactions have been decomposed using the natural orbital for the chemical valence framework and the bond components quantified through the charge displacement analysis. This methodology provides the quantification of the Dewar-Chatt-Duncanson (DCD) components for the Au-C and Au-Se bonds in the absence and presence of the second-sphere HB. The results presented here show that the anion has a dual mode action: it modifies the conformation of the cation by ion pairing (and this already influences the DCD components) and it induces new polarization effects that depend on the relative anion/cation relative orientation. The perchlorate polarizes SeU, enhancing the Se → Au σ donation and the Au → C back-donation and depressing the C → Au σ donation. On the contrary, the hexafluorophosphate depresses both the Se → Au and C → Au σ donations.
Collapse
|
19
|
Patti A, Pedotti S, Mazzeo G, Longhi G, Abbate S, Paoloni L, Bloino J, Rampino S, Barone V. Ferrocenes with simple chiral substituents: an in-depth theoretical and experimental VCD and ECD study. Phys Chem Chem Phys 2019; 21:9419-9432. [DOI: 10.1039/c9cp00437h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ferrocenes bearing chiral pendants are investigated through VCD and ECD. The VCD spectra are best interpreted by GVPT2-anharmonic DFT calculations. Diagnostic bands related to the absolute configuration of the title compounds are found in both kinds of spectra.
Collapse
Affiliation(s)
- Angela Patti
- Institute of Biomolecular Chemistry – CNR
- 95126 Catania
- Italy
| | - Sonia Pedotti
- Institute of Biomolecular Chemistry – CNR
- 95126 Catania
- Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT)
- Università di Brescia
- 25123 Brescia
- Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT)
- Università di Brescia
- 25123 Brescia
- Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale (DMMT)
- Università di Brescia
- 25123 Brescia
- Italy
| | | | - Julien Bloino
- Scuola Normale Superiore
- I-56126 Pisa
- Italy
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica dei Composti OrganoMetallici (CNR-ICCOM) Area della Ricerca CNR
| | | | | |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Licari D, Fusè M, Salvadori A, Tasinato N, Mendolicchio M, Mancini G, Barone V. Towards the SMART workflow system for computational spectroscopy. Phys Chem Chem Phys 2018; 20:26034-26052. [DOI: 10.1039/c8cp03417f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Is it possible to convert highly specialized research in the field of computational spectroscopy into robust and user-friendly aids to experiments and industrial applications?
Collapse
Affiliation(s)
- Daniele Licari
- Scuola Normale Superiore
- 56126 Pisa
- Italy
- Istituto Italiano di Tecnologia
- 16163 Genova
| | | | | | | | | | | | | |
Collapse
|