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Computational Spectroscopy 2020

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Physical Chemistry".

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 21155

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Dr. Paulo Ribeiro-Claro

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Guest Editor

CICECO - Aveiro Institute of Materials and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
Interests: molecular and supramolecular Structure; molecular modelling; momputational spectroscopy (computationally-assisted analysis of spectra)

Dr. Mariela Nolasco

E-Mail Website
Guest Editor

Department of Chemistry, Universidade de Aveiro, Aveiro, Portugal
Interests: molecular spectroscopy (vibrational, photoluminescence, and inelastic neutron scattering); luminescent materials; intramolecular energy transfer; DFT; TD-DFT; periodic calculations
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Special Issue Information

Dear Colleagues,

It is our great pleasure to invite you to submit an article for a high-profile Special Issue of Molecules on the theme “Computational Spectroscopy”.

For the past 50 years or so, computational chemistry and spectroscopy have shared a common path in their success histories. In its infancy, the computational approach often found support with respect to experimental spectroscopy. As computational techniques matured, spectroscopy started to reap great benefits from the information provided by calculations. To this day, the paths of spectroscopy and computational chemistry remain intertwined in an iterative process where one both challenges and reinforces the other’s growth.

The development of the computational tools currently available to support spectroscopic analysis is remarkable (from static to dynamic simulations, from single-molecule to periodic systems, from molecular mechanics to ab initio approaches), and examples of this fruitful collaboration are widespread and truly multidisciplinary.

The Special Issue “Computational Chemistry” will bring together contributions from all aspects of this synergistic collaboration between computational chemistry and spectroscopy. Thus, it will provide the readers the opportunity to easily obtain a bird’s-eye view of the state of the art in the field, while offering authors the chance to showcase their research work in a high-visibility platform.

Manuscripts describing original research, perspectives, and reviews focusing on the combined computational and spectroscopic approach will be welcome in this Special Issue of Molecules.

Dr. Paulo Ribeiro-Claro
Dr. Mariela Nolasco
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

Spectroscopy
Molecular and supramolecular structure
Crystal structure
Molecular modeling
Molecular simulation
Molecular Dynamics
Periodic methods
Density functional theory (DFT)
Time-dependent DFT (TD-DFT)

Published Papers (6 papers)

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Research

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7 pages, 1288 KiB

Open AccessArticle

Computational and Spectroscopic Studies of Carbon Disulfide

by Indri B. Adilina, Fauzan Aulia, Muhammad A. Fitriady, Ferensa Oemry, Robert R. Widjaya and Stewart F. Parker

Molecules 2020, 25(8), 1901; https://doi.org/10.3390/molecules25081901 - 20 Apr 2020

Cited by 3 | Viewed by 2590

Abstract

The vibrational spectroscopy of CS₂ has been investigated many times in all three phases. However, there is still some ambiguity about the location of two of the modes in the solid state. The aim of this work was to locate all of the modes by inelastic neutron scattering (INS) spectroscopy, (which has no selection rules), and to use periodic density functional theory to provide a complete and unambiguous assignment of all the modes in the solid state. A comparison of the observed and calculated INS spectra shows generally good agreement. All four of the ν₂ bending mode components are calculated to fall within 14 cm⁻¹. Inspection of the spectrum shows that there are no bands close to the intense feature at 390 cm⁻¹ (assigned to ν₂); this very strongly indicates that the A_u mode is within the envelope of the 390 cm⁻¹ band. Based on a simulation of the band shape of the 390 cm⁻¹ feature, the most likely position of the optically forbidden component of the ν₂ bending mode is 393 ± 2 cm⁻¹. The calculations show that the optically inactive A_u translational mode is strongly dispersed, so it does not result in a single feature in the INS spectrum. Full article

(This article belongs to the Special Issue Computational Spectroscopy 2020)

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16 pages, 4381 KiB

Open AccessArticle

Understanding the Structure and Dynamics of Nanocellulose-Based Composites with Neutral and Ionic Poly(methacrylate) Derivatives Using Inelastic Neutron Scattering and DFT Calculations

by Carla Vilela, Carmen S. R. Freire, Catarina Araújo, Svemir Rudić, Armando J. D. Silvestre, Pedro D. Vaz, Paulo J. A. Ribeiro-Claro and Mariela M. Nolasco

Molecules 2020, 25(7), 1689; https://doi.org/10.3390/molecules25071689 - 07 Apr 2020

Cited by 11 | Viewed by 2438

Abstract

Bacterial nanocellulose (BC)-based composites containing poly(2-hydroxyethyl methacrylate) (PHEMA), poly(methacroylcholine chloride) (PMACC) or poly(methacroylcholine hydroxide) (PMACH) were characterized by inelastic neutron scattering (INS) spectroscopy, combined with DFT (density functional theory) calculations of model systems. A reasonable match between calculated and experimental spectral lines and their intensities was used to support the vibrational assignment of the observed bands and to validate the possible structures. The differences between the spectra of the nanocomposites and the pure precursors indicate that interactions between the components are stronger for the ionic poly(methacrylate) derivatives than for the neutral counterpart. Displaced anions interact differently with cellulose chains, due to the different ability to compete with the O–H···O hydrogen bonds in cellulose. Hence, the INS is an adequate technique to delve deeper into the structure and dynamics of nanocellulose-based composites, confirming that they are true nanocomposite materials instead of simple mixtures of totally independent domains. Full article

(This article belongs to the Special Issue Computational Spectroscopy 2020)

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12 pages, 2318 KiB

Open AccessFeature PaperArticle

Vibrational Dynamics of Crystalline 4-Phenylbenzaldehyde from INS Spectra and Periodic DFT Calculations

by Mariela M. Nolasco, Catarina F. Araujo, Pedro D. Vaz, Ana M. Amado and Paulo Ribeiro-Claro

Molecules 2020, 25(6), 1374; https://doi.org/10.3390/molecules25061374 - 18 Mar 2020

Cited by 7 | Viewed by 2500

Abstract

The present work emphasizes the value of periodic density functional theory (DFT) calculations in the assessment of the vibrational spectra of molecular crystals. Periodic calculations provide a nearly one-to-one match between the calculated and observed bands in the inelastic neutron scattering (INS) spectrum of crystalline 4-phenylbenzaldehyde, thus validating their assignment and correcting previous reports based on single molecule calculations. The calculations allow the unambiguous assignment of the phenyl torsional mode at ca. 118–128 cm⁻¹, from which a phenyl torsional barrier of ca. 4000 cm⁻¹ is derived, and the identification of the collective mode involving the antitranslational motion of CH···O bonded pairs, a hallmark vibrational mode of systems where C-H···O contacts are an important feature. Full article

(This article belongs to the Special Issue Computational Spectroscopy 2020)

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15 pages, 3183 KiB

Open AccessArticle

Structure and Dynamics of the Superprotonic Conductor Caesium Hydrogen Sulfate, CsHSO₄

by Stewart F. Parker, Hamish Cavaye and Samantha K. Callear

Molecules 2020, 25(6), 1271; https://doi.org/10.3390/molecules25061271 - 11 Mar 2020

Cited by 4 | Viewed by 2784

Abstract

We have investigated caesium hydrogen sulfate, CsHSO₄, in all three of its ambient pressure phases by total scattering neutron diffraction, inelastic neutron scattering (INS) and Raman spectroscopies and periodic density functional theory calculations. Above 140 °C, CsHSO₄ undergoes a phase transition to a superprotonic conductor that has potential application in intermediate temperature fuel cells. Total scattering neutron diffraction data clearly show that all the existing structures of this phase are unable to describe the local structure, because they have either partial occupancies of the atoms and/or non-physical O–H distances. Knowledge of the local structure is crucial because it is this that determines the conduction mechanism. Starting from one of the previous models, we have generated a new structure that has no partial occupancies and reasonable O–H distances. After geometry optimisation, the calculated radial distribution function is in reasonable agreement with the experimental data, as are the calculated and observed INS and Raman spectra. This work is particularly notable in that we have measured INS spectra in the O–H stretch region above room temperature, which is extremely rare. The INS spectra have the enormous advantage that the electrical anharmonicity that complicates the infrared spectra is absent and the stretch modes are plainly seen. Full article

(This article belongs to the Special Issue Computational Spectroscopy 2020)

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12 pages, 1407 KiB

Open AccessArticle

Intramolecular and Metal-to-Molecule Charge Transfer Electronic Resonances in the Surface-Enhanced Raman Scattering of 1,4-Bis((E)-2-(pyridin-4-yl)vinyl)naphthalene

by Isabel López-Tocón, Elizabeth Imbarack, Juan Soto, Santiago Sanchez-Cortes, Patricio Leyton and Juan Carlos Otero

Molecules 2019, 24(24), 4622; https://doi.org/10.3390/molecules24244622 - 17 Dec 2019

Cited by 6 | Viewed by 2947

Abstract

Electrochemical surface-enhanced Raman scattering (SERS) of the cruciform system 1,4-bis((E)-2-(pyridin-4-yl)vinyl)naphthalene (bpyvn) was recorded on nanostructured silver surfaces at different electrode potentials by using excitation laser lines of 785 and 514.5 nm. SERS relative intensities were analyzed on the basis of the resonance Raman vibronic theory with the help of DFT calculations. The comparison between the experimental and the computed resonance Raman spectra calculated for the first five electronic states of the Ag₂-bpyvn surface complex model points out that the selective enhancement of the SERS band recorded at about 1600 cm⁻¹, under 785 nm excitation, is due to a resonant Raman process involving a photoexcited metal-to-molecule charge transfer state of the complex, while the enhancement of the 1570 cm⁻¹ band using 514.5 nm excitation is due to an intramolecular π→π* electronic transition localized in the naphthalenyl framework, resulting in a case of surface-enhanced resonance Raman spectrum (SERRS). Thus, the enhancement of the SERS bands of bpyvn is controlled by a general chemical enhancement mechanism in which different resonance processes of the overall electronic structure of the metal-molecule system are involved. Full article

(This article belongs to the Special Issue Computational Spectroscopy 2020)

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Review

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20 pages, 3001 KiB

Open AccessReview

Synergistic Approach of Ultrafast Spectroscopy and Molecular Simulations in the Characterization of Intramolecular Charge Transfer in Push-Pull Molecules

by Barbara Patrizi, Concetta Cozza, Adriana Pietropaolo, Paolo Foggi and Mario Siciliani de Cumis

Molecules 2020, 25(2), 430; https://doi.org/10.3390/molecules25020430 - 20 Jan 2020

Cited by 24 | Viewed by 7188

Abstract

The comprehensive characterization of Intramolecular Charge Transfer (ICT) stemming in push-pull molecules with a delocalized π-system of electrons is noteworthy for a bespoke design of organic materials, spanning widespread applications from photovoltaics to nanomedicine imaging devices. Photo-induced ICT is characterized by structural reorganizations, which allows the molecule to adapt to the new electronic density distribution. Herein, we discuss recent photophysical advances combined with recent progresses in the computational chemistry of photoactive molecular ensembles. We focus the discussion on femtosecond Transient Absorption Spectroscopy (TAS) enabling us to follow the transition from a Locally Excited (LE) state to the ICT and to understand how the environment polarity influences radiative and non-radiative decay mechanisms. In many cases, the charge transfer transition is accompanied by structural rearrangements, such as the twisting or molecule planarization. The possibility of an accurate prediction of the charge-transfer occurring in complex molecules and molecular materials represents an enormous advantage in guiding new molecular and materials design. We briefly report on recent advances in ultrafast multidimensional spectroscopy, in particular, Two-Dimensional Electronic Spectroscopy (2DES), in unraveling the ICT nature of push-pull molecular systems. A theoretical description at the atomistic level of photo-induced molecular transitions can predict with reasonable accuracy the properties of photoactive molecules. In this framework, the review includes a discussion on the advances from simulation and modeling, which have provided, over the years, significant information on photoexcitation, emission, charge-transport, and decay pathways. Density Functional Theory (DFT) coupled with the Time-Dependent (TD) framework can describe electronic properties and dynamics for a limited system size. More recently, Machine Learning (ML) or deep learning approaches, as well as free-energy simulations containing excited state potentials, can speed up the calculations with transferable accuracy to more complex molecules with extended system size. A perspective on combining ultrafast spectroscopy with molecular simulations is foreseen for optimizing the design of photoactive compounds with tunable properties. Full article

(This article belongs to the Special Issue Computational Spectroscopy 2020)

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