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

Deadline for manuscript submissions: closed (30 November 2019) | Viewed by 25410

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Dr. Mauricio Alcolea Palafox

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Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
Interests: DFT study in biomolecules; anticancer drugs; antivirus; DNA structure; nucleosides
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Dear Colleagues,

DFT methods have become very popular today and have become an invaluable tool for many researchers across a range of disciplines. This is due to the pragmatic observation that it is less computationally intensive than other methods with similar accuracy, or even better in some cases, such as in the theoretical prediction of vibrational spectra. Thus, DFT methods have widespread applications for the investigation of the electronic structure and chemical processes of many systems, in special molecules and condensed phases, which is crucial for molecular design and chemical synthesis. DFT methods provide invaluable information, complementary to the experimental data, about molecular systems and processes, and thus they represent very powerful tools for the interpretation and understanding of experimental results.

Due to the importance of DFT methods and their extensive applications, unpublished manuscripts that report these applications to any organic, inorganic or organometallic system and their experimental values are welcome for this Special Issue. In addition, advances in theoretical methods will also be accepted.

Dr. Mauricio Alcolea Palafox
Guest Editor

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Keywords

Density functional theory
Quantum chemical calculations
Molecular design
Vibrational spectra simulations
Electronic properties

Published Papers (6 papers)

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Research

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15 pages, 4257 KiB

Open AccessArticle

Co-Adsorption of H₂O, OH, and Cl on Aluminum and Intermetallic Surfaces and Its Effects on the Work Function Studied by DFT Calculations

by Min Liu, Ying Jin, Jinshan Pan and Christofer Leygraf

Molecules 2019, 24(23), 4284; https://doi.org/10.3390/molecules24234284 - 25 Nov 2019

Cited by 12 | Viewed by 3780

Abstract

The energetics of adsorption of H₂O layers and H₂O layers partially replaced with OH or Cl on an Al(111) surface and on selected surfaces of intermetallic phases, Mg₂Si and Al₂Cu, was studied by first-principle calculations using the density function theory (DFT). The results show that H₂O molecules tended to bind to all investigated surfaces with an adsorption energy in a relatively narrow range, between –0.8 eV and –0.5 eV, at increased water coverage. This can be explained by the dominant role of networks of hydrogen bonds at higher H₂O coverage. On the basis of the work function, the calculated Volta potential data suggest that both intermetallic phases became less noble than Al(111); also, the Volta potential difference was larger than 1 V when the coverage of the Cl-containing ad-layer reached one monolayer. The energetics of H₂O dissociation and substitution by Cl as well as the corresponding work function of each surface were also calculated. The increase in the work function of the Al(111) surface was attributed to the oxidation effect during H₂O adsorption, whereas the decrease of the work function for the Mg₂Si(111)–Si surface upon H₂O adsorption was explained by atomic and electronic rearrangements in the presence of H₂O and Cl. Full article

(This article belongs to the Special Issue Recent Advances in DFT: Theory, Simulations and Applications)

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13 pages, 5246 KiB

Open AccessArticle

Zirconocene-Catalyzed Dimerization of α-Olefins: DFT Modeling of the Zr-Al Binuclear Reaction Mechanism

by Ilya Nifant’ev, Alexander Vinogradov, Alexey Vinogradov, Stanislav Karchevsky and Pavel Ivchenko

Molecules 2019, 24(19), 3565; https://doi.org/10.3390/molecules24193565 - 02 Oct 2019

Cited by 18 | Viewed by 3138

Abstract

Zirconocene-mediated selective dimerization of α-olefins usually occurs when precatalyst (η⁵-C₅H₅)₂ZrCl₂ is activated by minimal excess of methylalumoxane (MAO). In this paper, we present the results of density functional theory (DFT) simulation of the initiation, propagation, and termination stages of dimerization and oligomerization of propylene within the framework of Zr-Al binuclear mechanism at M-06x/DGDZVP level of theory. The results of the analysis of the reaction profiles allow to explain experimental facts such as oligomerization of α-olefins at high MAO/(η⁵-C₅H₅)₂ZrCl₂ ratios and increase of the selectivity of dimerization in the presence of R₂AlCl. The results of DFT simulations confirm the crucial role of the presence of chloride in the selectivity of dimerization. The molecular hydrogen was found in silico and proven experimentally as an effective agent that increases the rate and selectivity of dimerization. Full article

(This article belongs to the Special Issue Recent Advances in DFT: Theory, Simulations and Applications)

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13 pages, 23757 KiB

Open AccessArticle

Effect of Nitrogen Cation as “Electron Trap” at π-Linker on Properties for p-Type Photosensitizers: DFT Study

by Zhi-Dan Sun, Jiang-Shan Zhao, Xue-Hai Ju and Qi-Ying Xia

Molecules 2019, 24(17), 3134; https://doi.org/10.3390/molecules24173134 - 28 Aug 2019

Cited by 3 | Viewed by 2330

Abstract

On the basis of thieno(3,2-b)thiophene and dithieno[3,2-b:2′,3′-d]thiophene (T2 and T3 moieties) as π-linker, the A, D and S series dyes were designed to investigate the effect of the introducing N⁺ as an “electron trap” into T2 and T3 on the properties of the dyes. The optimized structures, electronic and optical properties were investigated by the density functional theory (DFT) and time-dependent DFT (TD-DFT). The results show that the properties of the dyes are sensitive to the N⁺ position in π-linkers. D series dyes with electron-withdrawing units located near the donor have better properties than the corresponding A series with the electron-withdrawing units located near the acceptor. For A and D series, the N⁺ modified dye named T2N+1-d displays the largest red shift of the UV–vis absorption, the maximum integral values of the adsorption-wavelength curves over the visible light, the highest light harvesting efficiency (LHE, 0.996), and the strongest adsorption energy (−44.33 kcal/mol). T2N+1-d also has a large driving force of hole injection (ΔG_inj, −0.74 eV), which results in a more efficient hole injection. Bearing a lengthier π-linker than T2N+1-d, the properties of T2N+1-s are further improved. T2N+1-d moiety or its increased conjugated derivatives may be a promising π-linker. Full article

(This article belongs to the Special Issue Recent Advances in DFT: Theory, Simulations and Applications)

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11 pages, 3014 KiB

Open AccessArticle

Research on the Effect of Carbon Defects on the Hydrophilicity of Coal Pyrite Surface from the Insight of Quantum Chemistry

by Peng Xi, Ruixin Ma and Wenli Liu

Molecules 2019, 24(12), 2285; https://doi.org/10.3390/molecules24122285 - 19 Jun 2019

Cited by 7 | Viewed by 2386

Abstract

To investigate the effect of carbon defects on the hydrophilicity of the whole surface of the coal pyrite, the adsorption of the single H₂O molecule at different sites of the coal pyrite surface was studied with the DFT calculation. It was found that, like the ideal pyrite, the single H₂O molecule can stably adsorb at the doping-position, the ortho-position and the meta-position of the coal pyrite. The covalent bond and anti-bond were formed between O (water molecule) and Fe (the coal pyrite) through the Fe 3d orbital and O 2p orbital. Meanwhile, the S–H bond was replaced by the C–H bond. But away from the carbon defect centre, the adsorption of the single H₂O molecule increased gradually and the Fe–O covalent bond strength between the single H₂O molecule and the pyrite strengthened, which eventually became close to that of the undoped coal pyrite surface. Full article

(This article belongs to the Special Issue Recent Advances in DFT: Theory, Simulations and Applications)

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19 pages, 3539 KiB

Open AccessArticle

Electron Donor and Acceptor Influence on the Nonlinear Optical Response of Diacetylene-Functionalized Organic Materials (DFOMs): Density Functional Theory Calculations

by Muhammad Khalid, Riaz Hussain, Ajaz Hussain, Bakhat Ali, Farrukh Jaleel, Muhammad Imran, Mohammed Ali Assiri, Muhammad Usman Khan, Saeed Ahmed, Saba Abid, Sadia Haq, Kaynat Saleem, Shumaila Majeed and Chaudhary Jahrukh Tariq

Molecules 2019, 24(11), 2096; https://doi.org/10.3390/molecules24112096 - 02 Jun 2019

Cited by 49 | Viewed by 4153

Abstract

Herein, we report the quantum chemical results based on density functional theory for the polarizability (α) and first hyperpolarizability (β) values of diacetylene-functionalized organic molecules (DFOM) containing an electron acceptor (A) unit in the form of nitro group and electron donor (D) unit in the form of amino group. Six DFOM 1–6 have been designed by structural tailoring of the synthesized chromophore 4,4′-(buta-1,3-diyne-1,4-diyl) dianiline (R) and the influence of the D and A moieties on α and β was explored. Ground state geometries, HOMO-LUMO energies, and natural bond orbital (NBO) analysis of all DFOM (R and 1–6) were explored through B3LYP level of DFT and 6-31G(d,p) basis set. The polarizability (α), first hyperpolarizability (β) values were computed using B3LYP (gas phase), CAM-B3LYP (gas phase), CAM-B3LYP (solvent DMSO) methods and 6-31G(d,p) basis set combination. UV-Visible analysis was performed at CAM-B3LYP/6-31G(d,p) level of theory. Results illustrated that much reduced energy gap in the range of 2.212–2.809 eV was observed in designed DFOM 1–6 as compared to parent molecule R (4.405 eV). Designed DFOM (except for 2 and 4) were found red shifted compared to parent molecule R. An absorption at longer wavelength was observed for 6 with 371.46 nm. NBO analysis confirmed the involvement of extended conjugation and as well as charge transfer character towards the promising NLO response and red shift of molecules under study. Overall, compound 6 displayed large <α> and β_tot, computed to be 333.40 (a.u.) (B3LYP gas), 302.38 (a.u.) (CAM-B3LYP gas), 380.46 (a.u.) (CAM-B3LYP solvent) and 24708.79 (a.u.), 11841.93 (a.u.), 25053.32 (a.u.) measured from B3LYP (gas), CAM-B3LYP (gas) and CAM-B3LYP (DMSO) methods respectively. This investigation provides a theoretical framework for conversion of centrosymmetric molecules into non-centrosymmetric architectures to discover NLO candidates for modern hi-tech applications. Full article

(This article belongs to the Special Issue Recent Advances in DFT: Theory, Simulations and Applications)

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50 pages, 18373 KiB

Open AccessEditor’s ChoiceReview

Coordination Ring-Opening Polymerization of Cyclic Esters: A Critical Overview of DFT Modeling and Visualization of the Reaction Mechanisms

by Ilya Nifant’ev and Pavel Ivchenko

Molecules 2019, 24(22), 4117; https://doi.org/10.3390/molecules24224117 - 14 Nov 2019

Cited by 45 | Viewed by 7998

Abstract

Ring-opening polymerization (ROP) of cyclic esters (lactones, lactides, cyclic carbonates and phosphates) is an effective tool to synthesize biocompatible and biodegradable polymers. Metal complexes effectively catalyze ROP, a remarkable diversity of the ROP mechanisms prompted the use of density functional theory (DFT) methods for simulation and visualization of the ROP pathways. Optimization of the molecular structures of the key reaction intermediates and transition states has allowed to explain the values of catalytic activities and stereocontrol events. DFT computation data sets might be viewed as a sound basis for the design of novel ROP catalysts and cyclic substrates, for the creation of new types of homo- and copolymers with promising properties. In this review, we summarized the results of DFT modeling of coordination ROP of cyclic esters. The importance to understand the difference between initiation and propagation stages, to consider the possibility of polymer–catalyst coordination, to figure out the key transition states, and other aspects of DFT simulation and visualization of ROP have been also discussed in our review. Full article

(This article belongs to the Special Issue Recent Advances in DFT: Theory, Simulations and Applications)

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