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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 (31 July 2023) | Viewed by 18801

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Dr. Dipankar Roy

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Department of Mechanical Engineering, University of Alberta, 10-203 Donadeo Innovation Centre for Engineering, 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
Interests: DFT; solvation models; machine learning; molecular simulation; quantum chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Theoretical and computational chemistry as a research field has grown to complement experiments and assumed the mantle of guiding force in predictions and explorations in the fields of chemistry, biology, drug design, and all the interdisciplinary areas encompassed by these three. A rapid development and accessibility of computational hardware, robust code developments, and parallel deployments of codes in these new hardware have helped theoretical and computational chemistry to grow in leaps and bounds. This Special Issue titled “Computational Investigation on Molecular Design, Structure, Reactivity, and Solvation“ aims to bring the latest developments in the research areas covering molecular structure and/or activity prediction, chemical reactivity problems, chemical processes in liquid media, machine learning, and artificial intelligence in (bio)chemical (re)activity predictions.

Dr. Dipankar Roy
Guest Editor

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Keywords

theoretical chemistry
quantum chemistry
reaction mechanism
solvation models
computational spectroscopy
chemical bonding and structures
excited states and photochemistry
molecular simulations and forcefields

Published Papers (12 papers)

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Research

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11 pages, 5002 KiB

Open AccessCommunication

Selective Noble Gas Inclusion in Pentagon-Dodecahedral X₂₀-Cages

by Christopher Weinert, Dušan Ćoćić, Ralph Puchta and Rudi van Eldik

Molecules 2023, 28(15), 5676; https://doi.org/10.3390/molecules28155676 - 27 Jul 2023

Cited by 1 | Viewed by 736

Abstract

Using DFT-based computational chemistry calculations (ωB97XD/def2-tzvp//ωB97XD/def2-svp/svpfit + ZPE(ωB97XD/def2-svp/svpfit)), binding energies of noble gases encapsulated in a series of dodecahedrane molecules (general formula: X₂₀H₂₀ where X = C, Si, Ge, Sn and Pb, and X₂₀ where X = N, P, As, Sb and Bi) were calculated to learn about the noble gas selectivity. Based on calculated binding energies, the Sn₂₀H₂₀ cage can best accommodate noble gases with a medium size radius (Ar and Kr), while the Pb₂₀H₂₀ dodecahedrane cage is best suited for noble gases with the larger radii (Xe and Rn). On the other hand, from the elements of the V main group of the periodic table, the Bi₂₀ cage has shown the best results to selectively encapsulate Ar and Kr, with the amounts of energy being released being −5.24 kcal/mol and −6.13 kcal/mol, respectively. By monitoring the geometric changes of all here-reported host cages upon encapsulating the noble gas guest, the host has shown minor to no flexibility, testifying to the high rigidity of the dodecahedrane structure which was further reflected in very high encapsulating energies. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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13 pages, 1299 KiB

Open AccessArticle

New Insights into Adsorption Properties of the Tubular Au₂₆ from AIMD Simulations and Electronic Interactions

by Ying Meng and Qiman Liu

Molecules 2023, 28(7), 2916; https://doi.org/10.3390/molecules28072916 - 24 Mar 2023

Viewed by 1091

Abstract

Recently, we revealed the electronic nature of the tubular Au₂₆ based on spherical aromaticity. The peculiar structure of the Au₂₆ could be an ideal catalyst model for studying the adsorptions of the Au nanotubes. However, through Google Scholar, we found that no one has reported connections between the structure and reactivity properties of Au₂₆. Here, three kinds of molecules are selected to study the fundamental adsorption behaviors that occur on the surface of Au₂₆. When one CO molecule is adsorbed on the Au₂₆, the σ-hole adsorption structure is quickly identified as belonging to a ground state energy, and it still maintains integrity at a temperature of 500 K, where σ donations and π-back donations take place; however, two CO molecules make the structure of Au₂₆ appear with distortions or collapse. When one H₂ is adsorbed on the Au₂₆, the H–H bond length is slightly elongated due to charge transfers to the anti-bonding σ* orbital of H₂. The Au₂₆-H₂ can maintain integrity within 100 fs at 300 K and the H₂ molecule starts moving away from the Au₂₆ after 200 fs. Moreover, the Au₂₆ can act as a Lewis base to stabilize the electron-deficient BH₃ molecule, and frontier molecular orbitals overlap between the Au₂₆ and BH₃. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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13 pages, 464 KiB

Open AccessArticle

Identifying Systematic Force Field Errors Using a 3D-RISM Element Counting Correction

by Lizet Casillas, Vahe M. Grigorian and Tyler Luchko

Molecules 2023, 28(3), 925; https://doi.org/10.3390/molecules28030925 - 17 Jan 2023

Cited by 1 | Viewed by 1135

Abstract

Hydration free energies of small molecules are commonly used as benchmarks for solvation models. However, errors in predicting hydration free energies are partially due to the force fields used and not just the solvation model. To address this, we have used the 3D reference interaction site model (3D-RISM) of molecular solvation and existing benchmark explicit solvent calculations with a simple element count correction (ECC) to identify problems with the non-bond parameters in the general AMBER force field (GAFF). 3D-RISM was used to calculate hydration free energies of all 642 molecules in the FreeSolv database, and a partial molar volume correction (PMVC), ECC, and their combination (PMVECC) were applied to the results. The PMVECC produced a mean unsigned error of

1.01 \pm 0.04 kcal / mol

and root mean squared error of

1.44 \pm 0.07 kcal / mol

, better than the benchmark explicit solvent calculations from FreeSolv, and required less than 15 s of computing time per molecule on a single CPU core. Importantly, parameters for PMVECC showed systematic errors for molecules containing Cl, Br, I, and P. Applying ECC to the explicit solvent hydration free energies found the same systematic errors. The results strongly suggest that some small adjustments to the Lennard–Jones parameters for GAFF will lead to improved hydration free energy calculations for all solvent models. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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13 pages, 1864 KiB

Open AccessArticle

Computational Quantification of the Zwitterionic/Quinoid Ratio of Phenolate Dyes for Their Solvatochromic Prediction

by Andrés Aracena and Moisés Domínguez

Molecules 2022, 27(24), 9023; https://doi.org/10.3390/molecules27249023 - 17 Dec 2022

Cited by 5 | Viewed by 1532

Abstract

Solvatochromic dyes are utilized in various chemical and biological media as chemical sensors. Unfortunately, there is no simple way to predict the type of solvatochromism based on the structure of the dye alone, which restricts their design and synthesis. The most important family of solvatochromic sensors, pyridinium phenolate dyes, has the strongest solvatochromism. Using a natural population analysis (NPA) of the natural bond orbitals (NBO) of the phenolate group in the frontier molecular orbitals, it is possible to calculate the relative polarity of the ground state and excited state and, thus to develop a model that can predict the three types of solvatochromism observed for this family: negative, positive, and inverted. This methodology has been applied to thirteen representative examples from the literature. Our results demonstrate that the difference in the electron density of the phenolate moiety in the frontier molecular orbitals is a simple and inexpensive theoretical indicator for calculating the relative polarity of the ground and excited states of a representative library of pyridinium phenolate sensors, and thus predicting their solvatochromism. Comparing the results with the bond length alternation (BLA) and bond order alternation (BOA) indices showed that the NPA/NBO method is a better way to predict solvatochromic behavior. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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11 pages, 1757 KiB

Open AccessArticle

Samarium Diiodide Acting on Acetone—Modeling Single Electron Transfer Energetics in Solution

by Luca Steiner, Andreas J. Achazi, Bess Vlaisavljevich, Pere Miro, Beate Paulus and Anne-Marie Kelterer

Molecules 2022, 27(24), 8673; https://doi.org/10.3390/molecules27248673 - 8 Dec 2022

Cited by 1 | Viewed by 1477

Abstract

Samarium diiodide is a versatile single electron transfer (SET) agent with various applications in organic chemistry. Lewis structures regularly insinuate the existence of a ketyl radical when samarium diiodide binds a carbonyl group. The study presented here investigates this electron transfer by the means of computational chemistry. All electron CASPT2 calculations with the inclusion of scalar relativistic effects predict an endotherm electron transfer from samarium diiodide to acetone. Energies calculated with the PBE0-D3(BJ) functional and a small core pseudopotential are in good agreement with CASPT2. The calculations confirm the experimentally measured increase of the samarium diiodide reduction potential through the addition of hexamethylphosphoramide also known as HMPA. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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11 pages, 7833 KiB

Open AccessArticle

Magnetic, Electronic, and Optical Studies of Gd-Doped WO₃: A First Principle Study

by Ali Bahadur, Tehseen Ali Anjum, Mah Roosh, Shahid Iqbal, Hamad Alrbyawi, Muhammad Abdul Qayyum, Zaheer Ahmad, Murefah Mana Al-Anazy, Eslam B. Elkaeed, Rami Adel Pashameah, Eman Alzahrani and Abd-ElAziem Farouk

Molecules 2022, 27(20), 6976; https://doi.org/10.3390/molecules27206976 - 17 Oct 2022

Cited by 10 | Viewed by 1930

Abstract

Tungsten trioxide (WO₃) is mainly studied as an electrochromic material and received attention due to N-type oxide-based semiconductors. The magnetic, structural, and optical behavior of pristine WO₃ and gadolinium (Gd)-doped WO₃ are being investigated using density functional theory. For exchange-correlation potential energy, generalized gradient approximation (GGA+U) is used in our calculations, where U is the Hubbard potential. The estimated bandgap of pure WO₃ is 2.5 eV. After the doping of Gd, some states cross the Fermi level, and WO₃ acts as a degenerate semiconductor with a 2 eV bandgap. Spin-polarized calculations show that the system is antiferromagnetic in its ground state. The WO₃ material is a semiconductor, as there is a bandgap of 2.5 eV between the valence and conduction bands. The Gd-doped WO₃’s band structure shows few states across the Fermi level, which means that the material is metal or semimetal. After the doping of Gd, WO₃ becomes the degenerate semiconductor with a bandgap of 2 eV. The energy difference between ferromagnetic (FM) and antiferromagnetic (AFM) configurations is negative, so the Gd-doped WO₃ system is AFM. The pure WO₃ is nonmagnetic, where the magnetic moment in the system after doping Gd is 9.5599575 μB. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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15 pages, 5483 KiB

Open AccessArticle

Indane Based Molecular Motors: UV-Switching Increases Number of Isomers

by Valeriy P. Shendrikov, Anna S. Alekseeva, Erik F. Kot, Konstantin S. Mineev, Daria S. Tretiakova, Abdulilah Ece and Ivan A. Boldyrev

Molecules 2022, 27(19), 6716; https://doi.org/10.3390/molecules27196716 - 9 Oct 2022

Viewed by 1438

Abstract

We describe azophenylindane based molecular motors (aphin-switches) which have two different rotamers of trans-configuration and four different rotamers of cis-configuration. The behaviors of these motors were investigated both experimentally and computationally. The conversion of aphin-switch does not yield single isomer but a mixture of these. Although the trans to cis conversion leads to the increase of the system entropy some of the cis-rotamers can directly convert to each other while others should convert via trans-configuration. The motion of aphin-switches resembles the work of a mixing machine with indane group serving as a base and phenol group serving as a beater. The aphin-switches presented herein may provide a basis for promising applications in advanced biological systems or particularly in cases where on demand disordering of molecular packing has value, such as lipid bilayers. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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13 pages, 2812 KiB

Open AccessArticle

Understanding the Liquid States of Cyclic Hydrocarbons Containing N, O, and S Atoms via the 3D-RISM-KH Molecular Solvation Theory

by Dipankar Roy and Andriy Kovalenko

Molecules 2022, 27(19), 6563; https://doi.org/10.3390/molecules27196563 - 4 Oct 2022

Viewed by 1532

Abstract

The 3D-reference interaction site model (3D-RISM) molecular solvation theory in combination with the Kovalenko–Hirata (KH) closure is extended to seven heterocyclic liquids to understand their liquid states and to test the performance of the theory in solvation free energy (SFE) calculations of solutes in select solvents. The computed solvent site distribution profiles were compared with the all-atom molecular dynamics (MD) simulations, showing comparable performances. The computational results were compared against the structural parameters for liquids, whenever available, as well as against the experimental SFEs. The liquids are found to have local ordered structures held together via weak interactions in both the RISM and MD simulations. The 3D-RISM-KH computed SFEs are in good agreement with the benchmark values for the tetrahydrothiophene-S,S-dioxide, and showed comparatively larger deviations in the case of the SFEs in the tetrahydrofuran continuum. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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27 pages, 6076 KiB

Open AccessArticle

Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π⁺ Stacking Interactions in Thymine-[C_nmim]Br (n = 2, 4, 6, 8, 10) Microhydrates

by Yanni Wang, Chaowu Dai, Wei Huang, Tingting Ni, Jianping Cao, Jiangmei Pang, Huining Wei and Chaojie Wang

Molecules 2022, 27(19), 6242; https://doi.org/10.3390/molecules27196242 - 22 Sep 2022

Cited by 1 | Viewed by 1705

Abstract

The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([C_nmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH₂O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH₂O-y[C_nmim]⁺-xBr⁻, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H₂O-Br⁻-1, T-3H₂O-[C_nmim]⁺-Br⁻-1, T-2H₂O-[C_nmim]⁺-2Br⁻-1, and T-1H₂O-2[C_nmim]⁺-2Br⁻-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[C_nmim]⁺) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br⁻) is front > top. The stability order for the different microhydrates is following T-5H₂O-1 < T-4H₂O-Br⁻-1 < T-3H₂O-[C_nmim]⁺-Br⁻-1 < T-2H₂O-[C_nmim]⁺-2Br⁻-1 < T-1H₂O-2[C_nmim]⁺-2Br⁻-1. A good linear relationship between binding E_B values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π⁺ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [C_nmim]⁺ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr⁻ complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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13 pages, 2804 KiB

Open AccessArticle

Binding of Vialinin A and p-Terphenyl Derivatives to Ubiquitin-Specific Protease 4 (USP4): A Molecular Docking Study

by Christian Bailly and Gérard Vergoten

Molecules 2022, 27(18), 5909; https://doi.org/10.3390/molecules27185909 - 11 Sep 2022

Cited by 3 | Viewed by 1549

Abstract

The para-terphenyl derivative vialinin A (Vi-A), isolated from Thelephora fungi, has been characterized as a potent inhibitor of the ubiquitin-specific protease 4 (USP4). Blockade of USP4 contributes to the anti-inflammatory and anticancer properties of the natural product. We have investigated the interaction of Vi-A with USP4 by molecular modeling, to locate the binding site (around residue V98 within the domain in USP segment) and to identify the binding process and interaction contacts. From this model, a series of 32 p-terphenyl compounds were tested as potential USP4 binders, mainly in the vialinin, terrestrin and telephantin series. We identified 11 compounds presenting a satisfactory USP4 binding capacity, including two fungal products, vialinin B and aurantiotinin A, with a more favorable empirical energy of USP4 interaction (ΔE) than the reference product Vi-A. The rare p-terphenyl aurantiotinin A, isolated from the basidiomycete T. aurantiotincta, emerged as a remarkable USP4 binder. Structure-binding relationships have been identified and discussed, to guide the future design of USP4 inhibitors based on the p-terphenyl skeleton. The docking study should help the identification of other protease inhibitors from fungus. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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13 pages, 3417 KiB

Open AccessArticle

The Distance between Minima of Electron Density and Electrostatic Potential as a Measure of Halogen Bond Strength

by Edem R. Chakalov, Elena Yu. Tupikina, Daniil M. Ivanov, Ekaterina V. Bartashevich and Peter M. Tolstoy

Molecules 2022, 27(15), 4848; https://doi.org/10.3390/molecules27154848 - 28 Jul 2022

Cited by 8 | Viewed by 1754

Abstract

In this study, we present results of a detailed topological analysis of electron density (ED) of 145 halogen-bonded complexes formed by various fluorine-, chlorine-, bromine-, and iodine-containing compounds with trimethylphosphine oxide, Me₃PO. To characterize the halogen bond (XB) strength, we used the complexation enthalpy, the interatomic distance between oxygen and halogen, as well as the typical set of electron density properties at the bond critical points calculated at B3LYP/jorge-ATZP level of theory. We show for the first time that it is possible to predict the XB strength based on the distance between the minima of ED and molecular electrostatic potential (ESP) along the XB path. The gap between ED and ESP minima exponentially depends on local electronic kinetic energy density at the bond critical point and tends to be a common limiting value for the strongest halogen bond. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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Review

Jump to: Research

9 pages, 861 KiB

Open AccessReview

Revisiting the Use of Quantum Chemical Calculations in LogP_{octanol-water} Prediction

by Dipankar Roy and Chandan Patel

Molecules 2023, 28(2), 801; https://doi.org/10.3390/molecules28020801 - 13 Jan 2023

Cited by 5 | Viewed by 2157

Abstract

The partition coefficients of drug and drug-like molecules between an aqueous and organic phase are an important property for developing new therapeutics. The predictive power of computational methods is used extensively to predict partition coefficients of molecules. The application of quantum chemical calculations is used to develop methods to develop structure–activity relationship models for such prediction, either based on molecular fragment methods, or via direct calculation of solvation free energy in solvent continuum. The applicability, merits, and shortcomings of these developments are revisited here. Full article

(This article belongs to the Special Issue Computational Investigation on Molecular Design, Structure, and Solvation)

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