Theoretical, Quantum and Computational Chemistry

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Applied Sciences applsci	2.5	5.3	2011	18.4 Days	CHF 2400
Inorganics inorganics	3.1	2.8	2013	15.8 Days	CHF 2200
Molecules molecules	4.2	7.4	1996	15.1 Days	CHF 2700
Quantum Reports quantumrep	-	3.3	2019	16.4 Days	CHF 1400
Symmetry symmetry	2.2	5.4	2009	17.3 Days	CHF 2400
International Journal of Molecular Sciences ijms	4.9	8.1	2000	16.8 Days	CHF 2900

12 pages, 2628 KiB

Open AccessArticle

Investigation of Structures, Stabilities, and Electronic and Magnetic Properties of Niobium Carbon Clusters Nb₇C_n (n = 1–7)

by Hui-Fang Li, Huai-Qian Wang, Jia-Ming Zhang, Lan-Xin Qin, Hao Zheng and Yong-Hang Zhang

Molecules 2024, 29(8), 1692; https://doi.org/10.3390/molecules29081692 - 9 Apr 2024

Cited by 5 | Viewed by 1183

Abstract

The geometrical structures, relative stabilities, and electronic and magnetic properties of niobium carbon clusters, Nb₇C_n (n = 1–7), are investigated in this study. Density functional theory (DFT) calculations, coupled with the Saunders Kick global search, are conducted to explore the [...] Read more.

The geometrical structures, relative stabilities, and electronic and magnetic properties of niobium carbon clusters, Nb₇C_n (n = 1–7), are investigated in this study. Density functional theory (DFT) calculations, coupled with the Saunders Kick global search, are conducted to explore the structural properties of Nb₇C_n (n = 1–7). The results regarding the average binding energy, second-order difference energy, dissociation energy, HOMO-LUMO gap, and chemical hardness highlight the robust stability of Nb₇C₃. Analysis of the density of states suggests that the molecular orbitals of Nb₇C_n primarily consist of orbitals from the transition metal Nb, with minimal involvement of C atoms. Spin density and natural population analysis reveal that the total magnetic moment of Nb₇C_n predominantly resides on the Nb atoms. The contribution of Nb atoms to the total magnetic moment stems mainly from the 4d orbital, followed by the 5p, 5s, and 6s orbitals. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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13 pages, 1967 KiB

Open AccessArticle

Selective Extraction and Determination of Hydrocortisone and Dexamethasone in Skincare Cosmetics: Analytical Interpretation Using Statistical Physics Formalism

by Fatma Aouaini, Nadia Bouaziz, Ahlem Cherif, Haifa A. Alyousef and Abdelmottaleb Ben Lamine

Appl. Sci. 2024, 14(5), 2077; https://doi.org/10.3390/app14052077 - 1 Mar 2024

Viewed by 1343

Abstract

Molecularly imprinted polymers (MIPs), as magnetic extraction adsorbents, are used for the selective, rapid determination and extraction of dexamethasone and hydrocortisone in skincare products. Therefore, in this paper, magnetic molecularly imprinted polymers (MMIPs) and magnetic non-molecularly imprinted polymers (MNIPs) were utilized as adsorbents [...] Read more.

Molecularly imprinted polymers (MIPs), as magnetic extraction adsorbents, are used for the selective, rapid determination and extraction of dexamethasone and hydrocortisone in skincare products. Therefore, in this paper, magnetic molecularly imprinted polymers (MMIPs) and magnetic non-molecularly imprinted polymers (MNIPs) were utilized as adsorbents to describe the adsorption phenomena of dexamethasone and hydrocortisone. This interpretation, based on a statistical physics theory, applies the multilayer model with saturation to comprehend the adsorption of the drugs. Results obtained via numerical simulation revealed that dexamethasone and hydrocortisone adsorption happens via a non-parallel orientation on the surfaces of MMIPs and MNIPs, and they also showed that the adsorption amount of the MMIPs for the template molecule was notably greater than that of the MNIPs at the same initial concentration. The adsorption energy values retrieved from the data analysis ranged between 7.65 and 15.77 kJ/mol, indicating that the extraction and determination of dexamethasone and hydrocortisone is a physisorption process. Moreover, the distribution of a site’s energy was calculated to confirm the physical nature of the interactions between adsorbate/adsorbent and the heterogeneity of the surfaces of the MMIPs and MNIPs. Finally, the thermodynamic interpretation confirmed the exothermicity and spontaneous nature of the adsorption of these drugs on the tested adsorbents. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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15 pages, 1367 KiB

Open AccessArticle

The Role of Bond Functions in Describing Intermolecular Electron Correlation for Van der Waals Dimers: A Study of (CH₄)₂ and Ne₂

by Bogdan Rutskoy, Georgiy Ozerov and Dmitry Bezrukov

Int. J. Mol. Sci. 2024, 25(3), 1472; https://doi.org/10.3390/ijms25031472 - 25 Jan 2024

Viewed by 1224

Abstract

We present a study of the intermolecular interactions in van der Waals complexes of methane and neon dimers within the framework of the CCSD method. This approach was implemented and applied to calculate and examine the behavior of the contracted two-particle reduced density [...] Read more.

We present a study of the intermolecular interactions in van der Waals complexes of methane and neon dimers within the framework of the CCSD method. This approach was implemented and applied to calculate and examine the behavior of the contracted two-particle reduced density matrix (2-RDM). It was demonstrated that the region near the minimum of the two-particle density matrix correlation part, corresponding to the primary bulk of the Coulomb hole contribution, exerts a significant influence on the dispersion interaction energetics of the studied systems. As a result, the bond functions approach was applied to improve the convergence performance for the intermolecular correlation energy results with respect to the size of the atomic basis. For this, substantial acceleration was achieved by introducing an auxiliary basis of bond functions centered on the minima of the 2-RDM. For both methane and neon dimers, this general conclusion was confirmed with a series of CCSD calculations for the 2-RDM and the correlation energies. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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16 pages, 4708 KiB

Open AccessArticle

Theoretical Study of the NO Reduction Mechanism on Biochar Surfaces Modified by Li and Na Single Adsorption and OH Co-Adsorption

by Qiong Su, Fang Ren, Mengmeng Lu, Jinqin Zhao, Xingchen Zhu, Tao Shen, Yan Shen, Yanbin Wang and Junxi Liang

Molecules 2024, 29(3), 574; https://doi.org/10.3390/molecules29030574 - 24 Jan 2024

Cited by 1 | Viewed by 1408

Abstract

Theoretical and experimental investigations have shown that biochar, following KOH activation, enhances the efficiency of NO removal. Similarly, NaOH activation also improves NO removal efficiency, although the underlying mechanism remains unclear. In this study, zigzag configurations were employed as biochar models. Density functional [...] Read more.

Theoretical and experimental investigations have shown that biochar, following KOH activation, enhances the efficiency of NO removal. Similarly, NaOH activation also improves NO removal efficiency, although the underlying mechanism remains unclear. In this study, zigzag configurations were employed as biochar models. Density functional theory (DFT) was utilized to examine how Li and Na single adsorption and OH co-adsorption affect the reaction pathways of NO reduction on the biochar surface. The rate constants for all reaction-determining steps (RDSs) within a temperature range of 200 to 1000 K were calculated using conventional transition state theory (TST). The results indicate a decrease in the activation energy for NO reduction reactions on biochar when activated by Li and Na adsorption, thus highlighting their beneficial role in NO reduction. Compared to the case with Na activation, Li-activated biochar exhibited superior performance in terms of the NO elimination rate. Furthermore, upon the adsorption of the OH functional group onto the Li-decorated and Na-decorated biochar models (LiOH-decorated and NaOH-decorated chars), the RDS energy barriers were higher than those of Li and Na single adsorption but easily overcome, suggesting effective NO reduction. In conclusion, Li-decorated biochar showed the highest reactivity due to its low RDS barrier and exothermic reaction on the surface. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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18 pages, 9483 KiB

Open AccessArticle

Gas Phase Conformation of Trisaccharides and Core Pentasaccharide: A Three-Step Tree-Based Sampling and Quantum Mechanical Computational Approach

by Dong Chen, Jianming Gao, Danting Zheng, Zhiheng Guo and Zuncheng Zhao

Molecules 2023, 28(24), 8093; https://doi.org/10.3390/molecules28248093 - 14 Dec 2023

Viewed by 1288

Abstract

As an important component of N-linked glycoproteins, the core pentasaccharide is highly crucial to the potential application prospect of glycoprotein. However, the gas phase conformation study is a challenging one due to the size and complexity of the molecule, together with the necessity [...] Read more.

As an important component of N-linked glycoproteins, the core pentasaccharide is highly crucial to the potential application prospect of glycoprotein. However, the gas phase conformation study is a challenging one due to the size and complexity of the molecule, together with the necessity to rely on quantum chemistry modeling for relevant energetics and structures. In this paper, the structures of the trisaccharides and core pentasaccharides in N-linked glycans in the gas phase were constructed by a three-step tree-based (TSTB) sampling. Since single point energies of all the conformers are calculated at the temperature of zero, it is necessary to evaluate the stability at a high temperature. We calculate the Gibbs free energies using the standard thermochemistry model (T = 298.15 K). For trimannose, the energetic ordering at 298.15 K can be strongly changed compared to 0 K. Moreover, two structures of trimannose with high energies at 0 K are considered to provide a much better match of IR vibration signatures with the low Gibbs free energies. On this basis, the core pentasaccharide was constructed in three ways. The building configurations of core pentasaccharide were optimized to obtain reasonable low-energy stable conformers. Fortunately, the lowest-energy structure of core pentasaccharide is eventually the minimum at 0 K and 298.15 K. Furthermore, spectrum analysis of core pentasaccharide was carried out. Although poorly resolved, its contour from the experiment was in qualitative correspondence with the computed IR spectrum associated with its minimum free energy structure. A large number of strongly and weakly hydrogen-bonded hydroxyl and acetylamino groups contribute to a highly congested set of overlapping bands. Compared with traditional conformation generators, the TSTB sampling is employed to efficiently and comprehensively obtain preferred conformers of larger saccharides with lower energy. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)
(This article belongs to the Section Computational and Theoretical Chemistry)

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17 pages, 2380 KiB

Open AccessArticle

Possible Roles of Transition Metal Cations in the Formation of Interstellar Benzene via Catalytic Acetylene Cyclotrimerization

by Tatsuhiro Murakami, Naoki Matsumoto, Takashi Fujihara and Toshiyuki Takayanagi

Molecules 2023, 28(21), 7454; https://doi.org/10.3390/molecules28217454 - 6 Nov 2023

Cited by 2 | Viewed by 1944

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous interstellar molecules. However, the formation mechanisms of PAHs and even the simplest cyclic aromatic hydrocarbon, benzene, are not yet fully understood. Recently, we reported the statistical and dynamical properties in the reaction mechanism of Fe⁺-catalyzed [...] Read more.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous interstellar molecules. However, the formation mechanisms of PAHs and even the simplest cyclic aromatic hydrocarbon, benzene, are not yet fully understood. Recently, we reported the statistical and dynamical properties in the reaction mechanism of Fe⁺-catalyzed acetylene cyclotrimerization, whereby three acetylene molecules are directly converted to benzene. In this study, we extended our previous work and explored the possible role of the complex of other 3d transition metal cations, TM⁺ (TM = Sc, Ti, Mn, Co, and Ni), as a catalyst in acetylene cyclotrimerization. Potential energy profiles for bare TM⁺-catalyst (TM = Sc and Ti), for TM⁺NC⁻-catalyst (TM = Sc, Ti, Mn, Co, and Ni), and for TM⁺-(H₂O)₈-catalyst (TM = Sc and Ti) systems were obtained using quantum chemistry calculations, including the density functional theory levels. The calculation results show that the scandium and titanium cations act as efficient catalysts in acetylene cyclotrimerization and that reactants, which contain an isolated acetylene and (C₂H₂)₂ bound to a bare (ligated) TM cation (TM = Sc and Ti), can be converted into a benzene–metal–cation product complex without an entrance barrier. We found that the number of electrons in the 3d orbitals of the transition metal cation significantly contributes to the catalytic efficiency in the acetylene cyclotrimerization process. On-the-fly Born–Oppenheimer molecular dynamics (BOMD) simulations of the Ti⁺-NC⁻ and Ti⁺-(H₂O)₈ complexes were also performed to comprehensively understand the nuclear dynamics of the reactions. The computational results suggest that interstellar benzene can be produced via acetylene cyclotrimerization reactions catalyzed by transition metal cation complexes. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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11 pages, 2130 KiB

Open AccessArticle

A Theoretical Study on the Underlying Factors of the Difference in Performance of Organic Solar Cells Based on ITIC and Its Isomers

by Si-Qi Huang, Li-Li Wang, Qing-Qing Pan, Zhi-Wen Zhao, Ying Gao and Zhong-Min Su

Molecules 2023, 28(19), 6968; https://doi.org/10.3390/molecules28196968 - 7 Oct 2023

Cited by 2 | Viewed by 1695

Abstract

Recently, non-fullerene-based organic solar cells (OSCs) have made great breakthroughs, and small structural differences can have dramatic impacts on the power conversion efficiency (PCE). We take ITIC and its isomers as examples to study their effects on the performance of OSCs. ITIC and [...] Read more.

Recently, non-fullerene-based organic solar cells (OSCs) have made great breakthroughs, and small structural differences can have dramatic impacts on the power conversion efficiency (PCE). We take ITIC and its isomers as examples to study their effects on the performance of OSCs. ITIC and NFBDT only differed in the side chain position, and they were used as models with the same donor molecule, PBDB-T, to investigate the main reasons for the difference in their performance in terms of theoretical methods. In this work, a detailed comparative analysis of the electronic structure, absorption spectra, open circuit voltage and interfacial parameters of the ITIC and NFBDT systems was performed mainly by combining the density functional theory/time-dependent density functional theory and molecular dynamics simulations. The results showed that the lowest excited state of the ITIC molecule possessed a larger ∆q and more hybrid FE/CT states, and PBDB-T/ITIC had more charge separation paths as well as a larger k_CS and smaller k_CR. The reason for the performance difference between PBDB-T/ITIC and PBDB-T/NFBDT was elucidated, suggesting that ITIC is a superior acceptor based on a slight modulation of the side chain and providing a guiding direction for the design of superior-performing small molecule acceptor materials. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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30 pages, 3178 KiB

Open AccessReview

Counting Polynomials in Chemistry: Past, Present, and Perspectives

by Dan-Marian Joița, Mihaela Aurelia Tomescu and Lorentz Jäntschi

Symmetry 2023, 15(10), 1815; https://doi.org/10.3390/sym15101815 - 23 Sep 2023

Cited by 3 | Viewed by 2259

Abstract

Counting polynomials find their way into chemical graph theory through quantum chemistry in two ways: as approximate solutions to the Schrödinger equation or by storing information in a mathematical form and trying to find a pattern in the roots of these expressions. Coefficients [...] Read more.

Counting polynomials find their way into chemical graph theory through quantum chemistry in two ways: as approximate solutions to the Schrödinger equation or by storing information in a mathematical form and trying to find a pattern in the roots of these expressions. Coefficients count how many times a property occurs, and exponents express the extent of the property. They help understand the origin of regularities in the chemistry of specific classes of compounds. Our objective is to accelerate the research of newcomers into chemical graph theory. One problem in understanding these concepts is in the different approaches and notations of each research study; some researchers provide online tools for computing these mathematical concepts, but these need to be maintained for functionality. We take advantage of similar mathematical aspects of 14 such polynomials that merge theoretical chemistry and pure mathematics; give examples, differences, and similarities; and relate them to recent research. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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13 pages, 8193 KiB

Open AccessArticle

Decomposition of SO₂ on Ni(111) Surface and the Effect of Metal Doping: A First-Principles Study

by Lingtao Liu, Chenxin Zhang, Wenshou Wang, Genghong Li and Bingtian Zhu

Molecules 2023, 28(18), 6739; https://doi.org/10.3390/molecules28186739 - 21 Sep 2023

Cited by 3 | Viewed by 1373

Abstract

Sulfides poisoning of metallic Ni is an important issue in catalyst deactivation. SO₂, similar to H₂S and other sulfides, is an impurity presented in reactants or during the regeneration steps. Herein, spin-polarized density functional theory calculations were used to [...] Read more.

Sulfides poisoning of metallic Ni is an important issue in catalyst deactivation. SO₂, similar to H₂S and other sulfides, is an impurity presented in reactants or during the regeneration steps. Herein, spin-polarized density functional theory calculations were used to study the adsorption and decomposition of SO₂ on a pristine and metal-doped Ni(111) surface. The adsorption energy, transition state energy, and partial density of state (PDOS) were calculated. On the pristine Ni(111) surface, ten different configurations were considered, and three typical ones were selected for transition state searching. It was found that the reaction barrier of the first S-O bond dissociation was much higher than that of the second one. Doping the top layer with a second metal could strongly change the adsorption and decomposition behavior. Doping with 3/9ML Co slightly increases the adsorption energy of SO₂ for most configurations and decreases the reaction barriers of the SO₂-tht-2 decomposition, while the others decrease the adsorption ability and increase the barriers. The order of adsorption energy for the most stable configurations is Co > Ni > Cu > Rh > Pd. The order of the first S-O bond dissociation reaction barriers is Pd > Rh > Cu = Ni > Co, and the order of the second bond dissociation barrier is Rh > Pd > Cu > Ni > Co. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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12 pages, 2225 KiB

Open AccessArticle

Ab Initio Approach to the Structure, Vibrational Properties, and Electron Binding Energies of H₂S∙∙∙SO₂

by Isaac O. M. Magalhães, Benedito J. C. Cabral and João B. L. Martins

Molecules 2023, 28(18), 6656; https://doi.org/10.3390/molecules28186656 - 16 Sep 2023

Viewed by 1231

Abstract

The present study employs high-level ab initio calculations to investigate the structure, vibrational frequencies, and electronic properties of H₂S∙∙∙SO₂. The analysis of vibrational frequencies reveals an intramolecular vibrational energy transfer phenomenon, where energy from the stretching modes of H [...] Read more.

The present study employs high-level ab initio calculations to investigate the structure, vibrational frequencies, and electronic properties of H₂S∙∙∙SO₂. The analysis of vibrational frequencies reveals an intramolecular vibrational energy transfer phenomenon, where energy from the stretching modes of H₂S is transferred to the ν1s mode of SO₂. At the CCSD(T)/aug-cc-pVQZ level, the interaction energy between H₂S and SO₂ is predicted to be 2.78 kcal/mol. Electron propagator theory calculations yield a HOMO–LUMO gap of 8.24 eV for H₂S∙∙∙SO₂. Furthermore, by utilizing ab initio results for the adiabatic ionization energy and electron affinity, the electrophilicity of H₂S∙∙∙SO₂ is estimated to be 2.01 eV. This value is similar to the electrophilicity of SO₂, suggesting comparable reactivity and chemical behavior. The non-covalent interaction (NCI) analysis of the H₂S∙∙∙SO₂ complex emphasizes the significant contribution of non-covalent van der Waals interactions in its energetic stabilization. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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21 pages, 6844 KiB

Open AccessArticle

Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations

by Roberto Improta

Int. J. Mol. Sci. 2023, 24(16), 12614; https://doi.org/10.3390/ijms241612614 - 9 Aug 2023

Cited by 3 | Viewed by 1562

Abstract

I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)

^{+}

pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH

^{+}

), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important [...] Read more.

I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)

^{+}

pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH

^{+}

), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)

^{+}

core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical–physical effects. We show that the main photophysical paths involve C and CH

^{+}

bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH

^{+}

charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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22 pages, 6008 KiB

Open AccessArticle

Effect of Substituents on Molecular Reactivity during Lignin Oxidation by Chlorine Dioxide: A Density Functional Theory Study

by Baojie Liu, Lu Liu, Xin Qin, Yi Liu, Rui Yang, Xiaorong Mo, Chengrong Qin, Chen Liang and Shuangquan Yao

Int. J. Mol. Sci. 2023, 24(14), 11809; https://doi.org/10.3390/ijms241411809 - 22 Jul 2023

Cited by 6 | Viewed by 2080

Abstract

Lignin is a polymer with a complex structure. It is widely present in lignocellulosic biomass, and it has a variety of functional group substituents and linkage forms. Especially during the oxidation reaction, the positioning effect of the different substituents of the benzene ring [...] Read more.

Lignin is a polymer with a complex structure. It is widely present in lignocellulosic biomass, and it has a variety of functional group substituents and linkage forms. Especially during the oxidation reaction, the positioning effect of the different substituents of the benzene ring leads to differences in lignin reactivity. The position of the benzene ring branched chain with respect to methoxy is important. The study of the effect of benzene substituents on the oxidation reaction’s activity is still an unfinished task. In this study, density functional theory (DFT) and the m062x/6-311+g (d) basis set were used. Differences in the processes of phenolic oxygen intermediates formed by phenolic lignin structures (with different substituents) with chlorine dioxide during the chlorine dioxide reaction were investigated. Six phenolic lignin model species with different structures were selected. Bond energies, electrostatic potentials, atomic charges, Fukui functions and double descriptors of lignin model substances and reaction energy barriers are compared. The effects of benzene ring branched chains and methoxy on the mechanism of chlorine dioxide oxidation of lignin were revealed systematically. The results showed that the substituents with shorter branched chains and strong electron-absorbing ability were more stable. Lignin is not easily susceptible to the effects of chlorine dioxide. The substituents with longer branched chains have a significant effect on the flow of electron clouds. The results demonstrate that chlorine dioxide can affect the electron arrangement around the molecule, which directly affects the electrophilic activity of the molecule. The electron-absorbing effect of methoxy leads to a low dissociation energy of the phenolic hydroxyl group. Electrophilic reagents are more likely to attack this reaction site. In addition, the stabilizing effect of methoxy on the molecular structure of lignin was also found. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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14 pages, 3088 KiB

Open AccessArticle

Computational Investigation of Conformational Properties of Short Azapeptides: Insights from DFT Study and NBO Analysis

by Mouna El Khabchi, Mohammed Mcharfi, Mohammed Benzakour, Asmae Fitri, Adil Touimi Benjelloun, Jong-Won Song, Kang-Bong Lee and Ho-Jin Lee

Molecules 2023, 28(14), 5454; https://doi.org/10.3390/molecules28145454 - 17 Jul 2023

Cited by 1 | Viewed by 1543

Abstract

Azapeptides have gained much attention due to their ability to enhance the stability and bioavailability of peptide drugs. Their structural preferences, essential to understanding their function and potential application in the peptide drug design, remain largely unknown. In this work, we systematically investigated [...] Read more.

Azapeptides have gained much attention due to their ability to enhance the stability and bioavailability of peptide drugs. Their structural preferences, essential to understanding their function and potential application in the peptide drug design, remain largely unknown. In this work, we systematically investigated the conformational preferences of three azaamino acid residues in tripeptide models, Ac-azaXaa-Pro-NHMe [Xaa = Asn (4), Asp (5), Ala (6)], using the popular DFT functionals, B3LYP and B3LYP-D3. A solvation model density (SMD) was used to mimic the solvation effect on the conformational behaviors of azapeptides in water. During the calculation, we considered the impact of the amide bond in the azapeptide models on the conformational preferences of models 4–6. We analyzed the effect of the HB between the side-chain main chain and main-chain main-chain on the conformational behaviors of azapeptides 4–6. We found that the predicted lowest energy conformation for the three models differs depending on the calculation methods. In the gas phase, B3LYP functional indicates that the conformers tttANP-1 and tttADP-1 of azapeptides 4 and 5 correspond to the type I of β-turn, the lowest energy conformation with all-trans amide bonds. Considering the dispersion correction, B3LYP-D3 functional predicts the conformers tctANP-2 and tctADP-3 of azapeptide 4 and 5, which contain the cis amide bond preceding the Pro residue, as the lowest energy conformation in the gas phase. The results imply that azaAsx and Pro residues may involve cis-trans isomerization in the gas phase. In water, the predicted lowest energy conformer of azapeptides 4 and 5 differs from the gas phase results and depends on the calculational method. For azapeptide 6, regardless of calculation methods and phases, tttAAP-1 (β-I turn) is predicted as the lowest energy conformer. The results imply that the effect of the side chain that can form HBs on the conformational preferences of azapeptides 4 and 5 may not be negligible. We compared the theoretical results of azaXaa-Pro models with those of Pro-azaXaa models, showing that incorporating azaamino acid residue in peptides at different positions can significantly impact the folding patterns and stability of azapeptides. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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14 pages, 9531 KiB

Open AccessArticle

Investigation on the Mechanism of PAL (100) Surface Modified by APTES

by Weimin Jia, Bomiao Qi, Yanbin Wang, Zhibin Lu, Jiqian Wang, Qiong Su, Jingyan Nian and Junxi Liang

Molecules 2023, 28(14), 5417; https://doi.org/10.3390/molecules28145417 - 14 Jul 2023

Cited by 4 | Viewed by 1545

Abstract

The interfacial mechanism has always been a concern for 3-aminopropyltriethoxysilane (APTES)-grafted palygorskite (PAL). In this research, the mechanism of graft modification for grafting of APTES to the surface of PAL (100) was studied using density functional theory (DFT) calculation. The results illustrated that [...] Read more.

The interfacial mechanism has always been a concern for 3-aminopropyltriethoxysilane (APTES)-grafted palygorskite (PAL). In this research, the mechanism of graft modification for grafting of APTES to the surface of PAL (100) was studied using density functional theory (DFT) calculation. The results illustrated that different grafting states of the APTES influence the inter- and intramolecular interactions between APTES/PAL (100), which are reflected in the electronic structures. For single-, double-, and three-toothed state APTES-PAL (100), the charge transfer rates from the PAL (100) surface to APTES were 0.68, 1.02, and 0.77 e, respectively. The binding energy results show that PAL (100) modification performance in the double-tooth state is the best compared to the other states, with the lowest value of −181.91 kJ/mol. The double-toothed state has lower barrier energy (94.69, 63.11, and 153.67 kJ/mol) during the modification process. This study offers theoretical insights into the chemical modification of the PAL (100) surface using APTES coupling agents, and can provide a guide for practical applications. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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14 pages, 2234 KiB

Open AccessArticle

Impact of the Protein Environment on Two-Photon Absorption Cross-Sections of the GFP Chromophore Anion Resolved at the XMCQDPT2 Level of Theory

by Vladislav R. Aslopovsky, Andrei V. Scherbinin, Nadezhda N. Kleshchina and Anastasia V. Bochenkova

Int. J. Mol. Sci. 2023, 24(14), 11266; https://doi.org/10.3390/ijms241411266 - 10 Jul 2023

Cited by 2 | Viewed by 2227

Abstract

The search for fluorescent proteins with large two-photon absorption (TPA) cross-sections and improved brightness is required for their efficient use in bioimaging. Here, we explored the impact of a single-point mutation close to the anionic form of the GFP chromophore on its TPA [...] Read more.

The search for fluorescent proteins with large two-photon absorption (TPA) cross-sections and improved brightness is required for their efficient use in bioimaging. Here, we explored the impact of a single-point mutation close to the anionic form of the GFP chromophore on its TPA activity. We considered the lowest-energy transition of EGFP and its modification EGFP T203I. We focused on a methodology for obtaining reliable TPA cross-sections for mutated proteins, based on conformational sampling using molecular dynamics simulations and a high-level XMCQDPT2-based QM/MM approach. We also studied the numerical convergence of the sum-over-states formalism and provide direct evidence for the applicability of the two-level model for calculating TPA cross-sections in EGFP. The calculated values were found to be very sensitive to changes in the permanent dipole moments between the ground and excited states and highly tunable by internal electric field of the protein environment. In the case of the GFP chromophore anion, even a single hydrogen bond was shown to be capable of drastically increasing the TPA cross-section. Such high tunability of the nonlinear photophysical properties of the chromophore anions can be used for the rational design of brighter fluorescent proteins for bioimaging using two-photon laser scanning microscopy. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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28 pages, 4138 KiB

Open AccessArticle

Methylammonium Tetrel Halide Perovskite Ion Pairs and Their Dimers: The Interplay between the Hydrogen-, Pnictogen- and Tetrel-Bonding Interactions

by Pradeep R. Varadwaj, Arpita Varadwaj, Helder M. Marques and Koichi Yamashita

Int. J. Mol. Sci. 2023, 24(13), 10554; https://doi.org/10.3390/ijms241310554 - 23 Jun 2023

Cited by 2 | Viewed by 2020

Abstract

The structural stability of the extensively studied organic–inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX₃ (MA = CH₃NH₃⁺; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an [...] Read more.

The structural stability of the extensively studied organic–inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX₃ (MA = CH₃NH₃⁺; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an organic cation (CH₃NH₃⁺) and an inorganic anion (TtX₃⁻). However, the basic understanding of the underlying chemical bonding interactions in these systems that link the ionic moieties together in complex configurations is still limited. In this study, ion pair models constituting the organic and inorganic ions were regarded as the repeating units of periodic crystal systems and density functional theory simulations were performed to elucidate the nature of the non-covalent interactions between them. It is demonstrated that not only the charge-assisted N–H···X and C–H···X hydrogen bonds but also the C–N···X pnictogen bonds interact to stabilize the ion pairs and to define their geometries in the gas phase. Similar interactions are also responsible for the formation of crystalline MATtX₃ in the low-temperature phase, some of which have been delineated in previous studies. In contrast, the Tt···X tetrel bonding interactions, which are hidden as coordinate bonds in the crystals, play a vital role in holding the inorganic anionic moieties (TtX₃⁻) together. We have demonstrated that each Tt in each [CH₃NH₃⁺•TtX₃⁻] ion pair has the capacity to donate three tetrel (σ-hole) bonds to the halides of three nearest neighbor TtX₃⁻ units, thus causing the emergence of an infinite array of 3D TtX₆⁴⁻ octahedra in the crystalline phase. The TtX₄⁴⁻ octahedra are corner-shared to form cage-like inorganic frameworks that host the organic cation, leading to the formation of functional tetrel halide perovskite materials that have outstanding optoelectronic properties in the solid state. We harnessed the results using the quantum theory of atoms in molecules, natural bond orbital, molecular electrostatic surface potential and independent gradient models to validate these conclusions. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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16 pages, 747 KiB

Open AccessArticle

Hydrogen-like Plasmas under Endohedral Cavity

by Saptarshi Chowdhury, Neetik Mukherjee and Amlan K. Roy

Quantum Rep. 2023, 5(2), 459-474; https://doi.org/10.3390/quantum5020030 - 30 May 2023

Cited by 6 | Viewed by 1918

Abstract

Over the past few decades, confined quantum systems have emerged to be a subject of considerable importance in physical, chemical and biological sciences. Under such stressed conditions, they display many fascinating and notable physical and chemical properties. Here we address this situation by [...] Read more.

Over the past few decades, confined quantum systems have emerged to be a subject of considerable importance in physical, chemical and biological sciences. Under such stressed conditions, they display many fascinating and notable physical and chemical properties. Here we address this situation by using two plasma models, namely a weakly coupled plasma environment mimicked by a Debye-Hückel potential (DHP) and an exponential cosine screened Coulomb potential (ECSCP). On the other hand, the endohedral confinement is achieved via a Woods-Saxon (WS) potential. The critical screening constant, dipole oscillator strength (OS) and polarizability are investigated for an arbitrary state. A Shannon entropy-based strategy has been invoked to study the phase transition here. An increase in Z leads to larger critical screening. Moreover, a detailed investigation reveals that there exists at least one bound state in such plasmas. Pilot calculations are conducted for some low-lying states (

ℓ = 1 - 5

) using a generalized pseudo spectral scheme, providing optimal, non-uniform radial discretization. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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15 pages, 2393 KiB

Open AccessArticle

Unveiling the Stereoselectivity and Regioselectivity of the [3+2] Cycloaddition Reaction between N-methyl-C-4-methylphenyl-nitrone and 2-Propynamide from a MEDT Perspective

by Sabir A. Mohammed Salih, Huda A. Basheer, Jesus Vicente de Julián-Ortiz and Haydar A. Mohammad-Salim

Int. J. Mol. Sci. 2023, 24(10), 9102; https://doi.org/10.3390/ijms24109102 - 22 May 2023

Cited by 3 | Viewed by 2014

Abstract

[3+2] cycloaddition reactions play a crucial role in synthesizing complex organic molecules and have significant applications in drug discovery and materials science. In this study, the [3+2] cycloaddition (32CA) reactions of N-methyl-C-4-methyl phenyl-nitrone 1 and 2-propynamide 2, which have not been extensively [...] Read more.

[3+2] cycloaddition reactions play a crucial role in synthesizing complex organic molecules and have significant applications in drug discovery and materials science. In this study, the [3+2] cycloaddition (32CA) reactions of N-methyl-C-4-methyl phenyl-nitrone 1 and 2-propynamide 2, which have not been extensively studied before, were investigated using molecular electron density theory (MEDT) at the B3LYP/6–311++G(d,p) level of theory. According to an electron localization function (ELF) study, N-methyl-C-4-methyl phenyl-nitrone 1 is a zwitterionic species with no pseudoradical or carbenoid centers. Conceptual density functional theory (CDFT) indices were used to predict the global electronic flux from the strong nucleophilic N-methyl-C-4-methyl phenylnitrone 1 to the electrophilic 2-propynamide 2 functions. The 32CA reactions proceeded through two pairs of stereo- and regioisomeric reaction pathways to generate four different products: 3, 4, 5, and 6. The reaction pathways were irreversible owing to their exothermic characters: −136.48, −130.08, −130.99, and −140.81 kJ mol⁻¹, respectively. The enthalpy of the 32CA reaction leading to the formation of cycloadduct 6 was lower compared with the other path owing to a slight increase in its polar character, observed through the global electron density transfer (GEDT) during the transition states and along the reaction path. A bonding evolution theory (BET) analysis showed that these 32CA reactions proceed through the coupling of pseudoradical centers, and the formation of new C-C and C-O covalent bonds did not begin in the transition states. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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14 pages, 2334 KiB

Open AccessArticle

Fine Tuning the Intermolecular Interactions of Water Clusters Using the Dispersion-Corrected Density Functional Theory

by Alfonso Ferretti, Laura Canal, Robert A. Sorodoc, Sourab Sinha and Giuseppe Brancato

Molecules 2023, 28(9), 3834; https://doi.org/10.3390/molecules28093834 - 30 Apr 2023

Cited by 6 | Viewed by 2608

Abstract

Dispersion-inclusive density functional theory (DFT) methods have unequivocally demonstrated improved performances with respect to standard DFT approximations for modeling large and extended molecular systems at the quantum mechanical level. Yet, in some cases, disagreements with highly accurate reference calculations, such as CCSD(T) and [...] Read more.

Dispersion-inclusive density functional theory (DFT) methods have unequivocally demonstrated improved performances with respect to standard DFT approximations for modeling large and extended molecular systems at the quantum mechanical level. Yet, in some cases, disagreements with highly accurate reference calculations, such as CCSD(T) and quantum Monte Carlo (MC) calculations, still remain. Furthermore, the application of general-purpose corrections, such as the popular Grimme’s semi-classical models (DFT-D), to different Kohn–Sham exchange–correlation functionals sometimes leads to variable and inconsistent results, which recommend a careful prior evaluation. In a recent study, we proposed a simple optimization protocol for enhancing the accuracy of these DFT-D methods by following an alternative and system-specific approach. Here, adopting the same computational strategy, we show how the accurate MC intermolecular interactions of a large set of water clusters of variable sizes (i.e., 300 (H₂O)_n structures, n = 9, 15, 27) can be reproduced remarkably well by dispersion-corrected DFT models (i.e., B3LYP-D4, PBE-D4, revPBE(0)-D4) upon re-optimization, reaching a mean absolute error per monomer of ~0.1 kcal/mol. Hence, the obtained results support the use of this procedure for fine-tuning tailored DFT-D models for the accurate description of targeted molecular systems. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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16 pages, 1550 KiB

Open AccessArticle

Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field

by Bruno Zêzere, Tiago V. B. Fonseca, Inês Portugal, Mário M. Q. Simões, Carlos M. Silva and José R. B. Gomes

Int. J. Mol. Sci. 2023, 24(8), 7316; https://doi.org/10.3390/ijms24087316 - 15 Apr 2023

Cited by 3 | Viewed by 2239

Abstract

Molecular dynamics simulations employing the all-atom optimized potential for liquid simulations (OPLS-AA) force field were performed for determining self-diffusion coefficients (

D_{11}

) of ethanol and tracer diffusion coefficients (

D_{12}

) of solutes in ethanol at several temperature and pressure [...] Read more.

Molecular dynamics simulations employing the all-atom optimized potential for liquid simulations (OPLS-AA) force field were performed for determining self-diffusion coefficients (

D_{11}

) of ethanol and tracer diffusion coefficients (

D_{12}

) of solutes in ethanol at several temperature and pressure conditions. For simulations employing the original OPLS-AA diameter of ethanol’s oxygen atom (

σ_{OH}

), calculated and experimental diffusivities of protic solutes differed by more than 25%. To correct this behavior, the

σ_{OH}

was reoptimized using the experimental

D_{12}

of quercetin and of gallic acid in liquid ethanol as benchmarks. A substantial improvement of the calculated diffusivities was found by changing

σ_{OH}

from its original value (0.312 nm) to 0.306 nm, with average absolute relative deviations (AARD) of 3.71% and 4.59% for quercetin and gallic acid, respectively. The new

σ_{OH}

value was further tested by computing

D_{12}

of ibuprofen and butan-1-ol in liquid ethanol with AARDs of 1.55% and 4.81%, respectively. A significant improvement was also obtained for the

D_{11}

of ethanol with AARD = 3.51%. It was also demonstrated that in the case of diffusion coefficients of non-polar solutes in ethanol, the original

σ_{OH} = 0.312

nm should be used for better agreement with experiment. If equilibrium properties such as enthalpy of vaporization and density are estimated, the original diameter should be once again adopted. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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24 pages, 8912 KiB

Open AccessArticle

The Tetrel Bond and Tetrel Halide Perovskite Semiconductors

by Pradeep R. Varadwaj, Arpita Varadwaj, Helder M. Marques and Koichi Yamashita

Int. J. Mol. Sci. 2023, 24(7), 6659; https://doi.org/10.3390/ijms24076659 - 3 Apr 2023

Cited by 5 | Viewed by 2268

Abstract

The ion pairs [Cs⁺•TtX₃⁻] (Tt = Pb, Sn, Ge; X = I, Br, Cl) are the building blocks of all-inorganic cesium tetrel halide perovskites in 3D, CsTtX₃, that are widely regarded as blockbuster materials for optoelectronic [...] Read more.

The ion pairs [Cs⁺•TtX₃⁻] (Tt = Pb, Sn, Ge; X = I, Br, Cl) are the building blocks of all-inorganic cesium tetrel halide perovskites in 3D, CsTtX₃, that are widely regarded as blockbuster materials for optoelectronic applications such as in solar cells. The 3D structures consist of an anionic inorganic tetrel halide framework stabilized by the cesium cations (Cs⁺). We use computational methods to show that the geometrical connectivity between the inorganic monoanions, [TtX₃⁻]_∞, that leads to the formation of the TtX₆⁴⁻ octahedra and the 3D inorganic perovskite architecture is the result of the joint effect of polarization and coulombic forces driven by alkali and tetrel bonds. Depending on the nature and temperature phase of these perovskite systems, the Tt···X tetrel bonds are either indistinguishable or somehow distinguishable from Tt–X coordinate bonds. The calculation of the potential on the electrostatic surface of the Tt atom in molecular [Cs⁺•TtX₃⁻] provides physical insight into why the negative anions [TtX₃⁻] attract each other when in close proximity, leading to the formation of the CsTtX₃ tetrel halide perovskites in the solid state. The inter-molecular (and inter-ionic) geometries, binding energies, and charge density-based topological properties of sixteen [Cs⁺•TtX₃⁻] ion pairs, as well as some selected oligomers [Cs⁺•PbI₃⁻]_n (n = 2, 3, 4), are discussed. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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17 pages, 3711 KiB

Open AccessArticle

Initial Response of Pentaerythritol Tetranitrate (PETN) under the Coupling Effect of Preheating, Shock and Defect via the Molecular Dynamics Simulations with the Multiscale Shock Technique Method

by Yaping Zhang, Tao Wang and Yuanhang He

Molecules 2023, 28(7), 2911; https://doi.org/10.3390/molecules28072911 - 24 Mar 2023

Cited by 3 | Viewed by 1916

Abstract

The initial response of PETN under the coupling of preheating, impact and defects was simulated by Multiscale Shock Technique (MSST) method and molecular dynamics. The temperature change of PETN during impact compression can be divided into three stages: (1) the elastoplastic change of [...] Read more.

The initial response of PETN under the coupling of preheating, impact and defects was simulated by Multiscale Shock Technique (MSST) method and molecular dynamics. The temperature change of PETN during impact compression can be divided into three stages: (1) the elastoplastic change of the system caused by initial compression; (2) part of PETN decomposes and releases energy to raise temperature; (3) a secondary chemical reaction occurs, resulting in rapid temperature rise. Under the given conditions, a higher initial preheating temperature will lead to faster decomposition of PETN; The existence of defects will accelerate the decomposition of PETN molecules; Coupling the highest preheating temperature with defects will lead to the fastest decomposition of PETN molecules, while in the defect-free PETN system with a preheating temperature of 300 K, the decomposition of PETN molecules is the slowest. For the case of U_s = 8 km·s⁻¹, the effect of defects on the initial PETN reaction is greater than the initial preheating temperature; When the impact velocity is greater than 9 km·s⁻¹, the impact velocity is an important factor affecting the decomposition of PETN molecules. For U_s = 10 km·s⁻¹, NO₂ is the main initial product in the defective PETN crystal, while in the perfect PETN crystal, it is the combination of NO₂ and HONO. The chemical reaction kinetics analysis shows that the preheating temperature and defects will accelerate the decomposition of PETN. The higher the preheating temperature, the faster the decomposition of PETN. For the case of U_s = 7 km·s⁻¹, 8 km·s⁻¹ and 9 km·s⁻¹, the existence of defects will increase the decomposition rate by more than 50% regardless of the initial preheating temperature. In the case of Us = 10 km·s⁻¹, the improvement of decomposition rate by defects is not as significant as the initial preheating temperature. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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26 pages, 7675 KiB

Open AccessArticle

A Comprehensive Investigation into the Crystallology, Molecule, and Quantum Chemistry Properties of Two New Hydrous Long-Chain Dibasic Ammonium Salts C_nH_2n+8N₂O₆ (n = 35 and 37)

by Zengbo Ke, Xinhui Fan, Youying Di, Fengying Chen, Xi Han, Ke Yang and Bing Li

Int. J. Mol. Sci. 2023, 24(6), 5467; https://doi.org/10.3390/ijms24065467 - 13 Mar 2023

Cited by 2 | Viewed by 2595 | Correction

Abstract

Through the salification reaction of carboxylation, successful attachment of the long-chain alkanoic acid to the two ends of 1,3-propanediamine was realized, which enabled the doubling of the long-chain alkanoic acid carbon chain. Hydrous 1,3-propanediamine dihexadecanoate (abbreviated as 3C16) and 1,3-propanediamine diheptadecanoate (abbreviated as [...] Read more.

Through the salification reaction of carboxylation, successful attachment of the long-chain alkanoic acid to the two ends of 1,3-propanediamine was realized, which enabled the doubling of the long-chain alkanoic acid carbon chain. Hydrous 1,3-propanediamine dihexadecanoate (abbreviated as 3C16) and 1,3-propanediamine diheptadecanoate (abbreviated as 3C17) were synthesized afterward, and their crystal structures were characterized by the X-ray single crystal diffraction technique. By analyzing their molecular and crystal structure, their composition, spatial structure, and coordination mode were determined. Two water molecules played important roles in stabilizing the framework of both compounds. Hirshfeld surface analysis revealed the intermolecular interactions between the two molecules. The 3D energy framework map presented the intermolecular interactions more intuitively and digitally, in which dispersion energy plays a dominant role. DFT calculations were performed to analyze the frontier molecular orbitals (HOMO–LUMO). The energy difference between the HOMO–LUMO is 0.2858 eV and 0.2855 eV for 3C16 and 3C17, respectively. DOS diagrams further confirmed the distribution of the frontier molecular orbitals of 3C16 and 3C17. The charge distributions in the compounds were visualized using a molecular electrostatic potential (ESP) surface. ESP maps indicated that the electrophilic sites are localized around the oxygen atom. The crystallographic data and parameters of quantum chemical calculation in this paper will provide data and theoretical support for the development and application of such materials. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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13 pages, 3506 KiB

Open AccessArticle

Theoretical Study on the Gas-Phase and Aqueous Interface Reaction Mechanism of Criegee Intermediates with 2-Methylglyceric Acid and the Nucleation of Products

by Lei Li, Qingzhu Zhang, Yuanyuan Wei, Qiao Wang and Wenxing Wang

Int. J. Mol. Sci. 2023, 24(6), 5400; https://doi.org/10.3390/ijms24065400 - 11 Mar 2023

Cited by 1 | Viewed by 2308

Abstract

Criegee intermediates (CIs) are important in the sink of many atmospheric substances, including alcohols, organic acids, amines, etc. In this work, the density functional theory (DFT) method was used to calculate the energy barriers for the reactions of CH₃CHOO with 2-methyl [...] Read more.

Criegee intermediates (CIs) are important in the sink of many atmospheric substances, including alcohols, organic acids, amines, etc. In this work, the density functional theory (DFT) method was used to calculate the energy barriers for the reactions of CH₃CHOO with 2-methyl glyceric acid (MGA) and to evaluate the interaction of the three functional groups of MGA. The results show that the reactions involving the COOH group of MGA are negligibly affected, and that hydrogen bonding can affect the reactions involving α-OH and β-OH groups. The water molecule has a negative effect on the reactions of the COOH group. It decreases the energy barriers of reactions involving the α-OH and β-OH groups as a catalyst. The Born-Oppenheimer molecular dynamic (BOMD) was applied to simulate the reactions of CH₃CHOO with MGA at the gas-liquid interface. Water molecule plays the role of proton transfer in the reaction. Gas-phase calculations and gas-liquid interface simulations demonstrate that the reaction of CH₃CHOO with the COOH group is the main pathway in the atmosphere. The molecular dynamic (MD) simulations suggest that the reaction products can form clusters in the atmosphere to participate in the formation of particles. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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11 pages, 5987 KiB

Open AccessCommunication

The Effects of Acid and Water in the Formation of Anodic Alumina: DFT and Experiment Study

by Zhengwei Zhang, Jin Kang, Xiaodong Li, Ping Li, Yali Du, Yufan Qin, Ningyi Li and Jiebin Li

Molecules 2023, 28(6), 2427; https://doi.org/10.3390/molecules28062427 - 7 Mar 2023

Viewed by 1447

Abstract

The DFT method is employed to study the adsorption and reaction behaviors of HC₂O₄⁻, H₂PO₄⁻, HSO₄⁻ and H₂O on neutral and anodic aluminum slabs. With the exception of adsorption, [...] Read more.

The DFT method is employed to study the adsorption and reaction behaviors of HC₂O₄⁻, H₂PO₄⁻, HSO₄⁻ and H₂O on neutral and anodic aluminum slabs. With the exception of adsorption, the three acid radicals can successively take the two H atoms from the adsorbed H₂O on the anodic aluminum slabs, which is the key step of the formation of anodic alumina. The dehydrogenation reaction is dominated by the Coulombic interaction of O and H, respectively belonging to acid radicals and the adsorbed H₂O or OH, rather than by the interaction of electronic orbits located on the two kinds of atoms. The experiment of anodic polarization of aluminum verifies the calculation result well. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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15 pages, 3277 KiB

Open AccessArticle

Theoretically Revealing the Response of Intermolecular Vibration Energy Transfer and Decomposition Process of the DNTF System to Electric Fields Using Two-Dimensional Infrared Spectra

by Haichao Ren, Linxiang Ji, Xianzhen Jia, Jun Tao, Ruipeng Liu, Dongqing Wei, Xiaofeng Wang and Guangfu Ji

Int. J. Mol. Sci. 2023, 24(5), 4352; https://doi.org/10.3390/ijms24054352 - 22 Feb 2023

Cited by 5 | Viewed by 2029

Abstract

The external electric field (E-field), which is an important stimulus, can change the decomposition mechanism and sensitivity of energetic materials. As a result, understanding the response of energetic materials to external E-fields is critical for their safe use. Motivated by recent experiments and [...] Read more.

The external electric field (E-field), which is an important stimulus, can change the decomposition mechanism and sensitivity of energetic materials. As a result, understanding the response of energetic materials to external E-fields is critical for their safe use. Motivated by recent experiments and theories, the two-dimensional infrared (2D IR) spectra of 3,4-bis (3-nitrofurazan-4-yl) furoxan (DNTF), which has a high energy, a low melting point, and comprehensive properties, were theoretically investigated. Cross-peaks were observed in 2D IR spectra under different E-fields, which demonstrated an intermolecular vibration energy transfer; the furazan ring vibration was found to play an important role in the analysis of vibration energy distribution and was extended over several DNTF molecules. Measurements of the non-covalent interactions, with the support of the 2D IR spectra, indicated that there were obvious non-covalent interactions among different DNTF molecules, which resulted from the conjugation of the furoxan ring and the furazan ring; the direction of the E-field also had a significant influence on the strength of the weak interactions. Furthermore, the calculation of the Laplacian bond order, which characterized the C-NO₂ bonds as trigger bonds, predicted that the E-fields could change the thermal decomposition process of DNTF while the positive E-field facilitates the breakdown of the C-NO₂ in DNTFⅣ molecules. Our work provides new insights into the relationship between the E-field and the intermolecular vibration energy transfer and decomposition mechanism of the DNTF system. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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9 pages, 1468 KiB

Open AccessCommunication

Optimal Complex Morlet Wavelet Parameters for Quantitative Time-Frequency Analysis of Molecular Vibration

by Shuangquan Li, Shangyi Ma and Shaoqing Wang

Appl. Sci. 2023, 13(4), 2734; https://doi.org/10.3390/app13042734 - 20 Feb 2023

Cited by 4 | Viewed by 4147

Abstract

When the complex Morlet function (CMOR) is used as a wavelet basis, it is necessary to select optimal bandwidth and center frequency. However, the method to select the optimal CMOR wavelet parameters for one specific frequency is still unclear. In this paper, we [...] Read more.

When the complex Morlet function (CMOR) is used as a wavelet basis, it is necessary to select optimal bandwidth and center frequency. However, the method to select the optimal CMOR wavelet parameters for one specific frequency is still unclear. In this paper, we deeply investigate the essence of CMOR wavelet transform and clearly illustrate the time-frequency resolution and edge effect. Then, the selection method of the optimal bandwidth and center frequency is proposed. We further perform the quantitative time-frequency (QTF) analysis of water molecule vibration based on our method. We find that the CMOR wavelet parameters obtained by our method can not only meet the requirement of frequency resolution but also meet the limit of edge effect. Moreover, there is an uphill energy relaxation in the vibration of the water molecule, which agrees well with the experimental results. These results demonstrate that our method can accurately find the optimal CMOR wavelet parameters for the target frequency. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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26 pages, 5434 KiB

Open AccessArticle

Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity

by Larissa Balabanova, Olga Nedashkovskaya, Nadezhda Otstavnykh, Marina Isaeva, Oksana Kolpakova, Iuliia Pentehina, Aleksandra Seitkalieva, Yulia Noskova, Varvara Stepochkina, Oksana Son and Liudmila Tekutyeva

Int. J. Mol. Sci. 2023, 24(4), 4158; https://doi.org/10.3390/ijms24044158 - 19 Feb 2023

Cited by 3 | Viewed by 2843

Abstract

Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa [...] Read more.

Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4′-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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11 pages, 2424 KiB

Open AccessArticle

Theoretical Study on the Gas Phase and Gas–Liquid Interface Reaction Mechanism of Criegee Intermediates with Glycolic Acid Sulfate

by Lei Li, Qingzhu Zhang, Yuanyuan Wei, Qiao Wang and Wenxing Wang

Int. J. Mol. Sci. 2023, 24(4), 3355; https://doi.org/10.3390/ijms24043355 - 8 Feb 2023

Cited by 2 | Viewed by 2359

Abstract

Criegee intermediates (CIs) are important zwitterionic oxidants in the atmosphere, which affect the budget of OH radicals, amines, alcohols, organic/inorganic acids, etc. In this study, quantum chemical calculation and Born–Oppenheimer molecular dynamic (BOMD) simulation were performed to show the reaction mechanisms of C2 [...] Read more.

Criegee intermediates (CIs) are important zwitterionic oxidants in the atmosphere, which affect the budget of OH radicals, amines, alcohols, organic/inorganic acids, etc. In this study, quantum chemical calculation and Born–Oppenheimer molecular dynamic (BOMD) simulation were performed to show the reaction mechanisms of C2 CIs with glycolic acid sulfate (GAS) at the gas-phase and gas–liquid interface, respectively. The results indicate that CIs can react with COOH and OSO₃H groups of GAS and generate hydroperoxide products. Intramolecular proton transfer reactions occurred in the simulations. Moreover, GAS acts as a proton donor and participates in the hydration of CIs, during which the intramolecular proton transfer also occurs. As GAS widely exists in atmospheric particulate matter, the reaction with GAS is one of the sink pathways of CIs in areas polluted by particulate matter. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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14 pages, 4283 KiB

Open AccessArticle

Theoretical Studies on Selectivity of HPK1/JAK1 Inhibitors by Molecular Dynamics Simulations and Free Energy Calculations

by Huizhen Ge, Chunchao Tang, Yiting Pan and Xiaojun Yao

Int. J. Mol. Sci. 2023, 24(3), 2649; https://doi.org/10.3390/ijms24032649 - 31 Jan 2023

Cited by 1 | Viewed by 2770

Abstract

Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of T cell receptor, which has been regarded as a potential target for immunotherapy. Yu et al. observed the off-target effect of the high-throughput screening HPK1 kinase inhibitor hits on JAK1 kinase. The off-target [...] Read more.

Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of T cell receptor, which has been regarded as a potential target for immunotherapy. Yu et al. observed the off-target effect of the high-throughput screening HPK1 kinase inhibitor hits on JAK1 kinase. The off-target effect is usually due to the lack of specificity of the drug, resulting in toxic side effects. Therefore, exploring the mechanisms to selectively inhibit HPK1 is critical for developing effective and safe inhibitors. In this study, two indazole compounds as HPK1 inhibitors with different selectivity towards JAK1 were used to investigate the selectivity mechanism using multiple computational methods, including conventional molecular dynamics simulations, binding free energy calculations and umbrella sampling simulations. The results indicate that the salt bridge between the inhibitor and residue Asp101 of HPK1 favors their selectivity towards HPK1 over JAK1. Information obtained from this study can be used to discover and design more potent and selective HPK1 inhibitors for immunotherapy. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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14 pages, 4500 KiB

Open AccessArticle

Exploring the Interdependence between Electronically Unfavorable Situations and Pressure in a Chalcogenide Superconductor

by Kai S. Fries and Simon Steinberg

Inorganics 2023, 11(2), 61; https://doi.org/10.3390/inorganics11020061 - 27 Jan 2023

Viewed by 1992

Abstract

The development of solids with the requested chemical and physical properties requires a thorough understanding of their electronic structures, as proper knowledge of the electronic structure of a given solid provides invaluable information regarding its properties. In this context, recent research on two [...] Read more.

The development of solids with the requested chemical and physical properties requires a thorough understanding of their electronic structures, as proper knowledge of the electronic structure of a given solid provides invaluable information regarding its properties. In this context, recent research on two competing sorts of electronic instabilities in chalcogenide superconductors stimulated us to explore the interdependence between these instabilities and another aspect, pressure, which was previously shown to influence the presence of a superconducting state in diverse solids. To accomplish our goal, we carried out pressure-dependent examinations of the electronic structures of two tellurides, YTe and YTe_0.97, which were inspected as prototypes in our explorations based on quantum-chemical means. In addition to our pressure-dependent explorations of the electronic structures, we also performed chemical bonding analyses to reveal the subtle interplay between pressure and two sorts of electronically unfavorable situations. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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11 pages, 1197 KiB

Open AccessArticle

In Silico Simulation of Impacts of Metal Nano-Oxides on Cell Viability in THP-1 Cells Based on the Correlation Weights of the Fragments of Molecular Structures and Codes of Experimental Conditions Represented by Means of Quasi-SMILES

by Alla P. Toropova, Andrey A. Toropov and Natalja Fjodorova

Int. J. Mol. Sci. 2023, 24(3), 2058; https://doi.org/10.3390/ijms24032058 - 20 Jan 2023

Viewed by 1929

Abstract

A simulation of the effect of metal nano-oxides at various concentrations (25, 50, 100, and 200 milligrams per millilitre) on cell viability in THP-1 cells (%) based on data on the molecular structure of the oxide and its concentration is proposed. We used [...] Read more.

A simulation of the effect of metal nano-oxides at various concentrations (25, 50, 100, and 200 milligrams per millilitre) on cell viability in THP-1 cells (%) based on data on the molecular structure of the oxide and its concentration is proposed. We used a simplified molecular input-line entry system (SMILES) to represent the molecular structure. So-called quasi-SMILES extends usual SMILES with special codes for experimental conditions (concentration). The approach based on building up models using quasi-SMILES is self-consistent, i.e., the predictive potential of the model group obtained by random splits into training and validation sets is stable. The Monte Carlo method was used as a basis for building up the above groups of models. The CORAL software was applied to building the Monte Carlo calculations. The average determination coefficient for the five different validation sets was R² = 0.806 ± 0.061. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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12 pages, 3232 KiB

Open AccessArticle

Nonoxidative Coupling of Methane to Produce C₂ Hydrocarbons on FLPs of an Albite Surface

by Yannan Zhou, Ye Chen, Xuegang Luo and Xin Wang

Molecules 2023, 28(3), 1037; https://doi.org/10.3390/molecules28031037 - 19 Jan 2023

Cited by 2 | Viewed by 1946

Abstract

The characteristics of active sites on the surface of albite were theoretically analyzed by density functional theory, and the activation of the C-H bond of methane using an albite catalyst and the reaction mechanism of preparing C₂ hydrocarbons by nonoxidative coupling were [...] Read more.

The characteristics of active sites on the surface of albite were theoretically analyzed by density functional theory, and the activation of the C-H bond of methane using an albite catalyst and the reaction mechanism of preparing C₂ hydrocarbons by nonoxidative coupling were studied. There are two frustrated Lewis pairs (FLPs) on the (001) and (010) surfaces of albite; they can dissociate H₂ under mild conditions and show high activity for the activation of methane C-H bonds. CH₄ molecules can undergo direct dissociative adsorption on the (010) surface, whereas a 50.07 kJ/mol activation barrier is needed on the (001) surface. The prepared albite catalyst has a double combination function of the (001) and (010) surfaces; these surfaces produce a spillover phenomenon in the process of CH₄ activation reactions, where CH₃ overflows from the (001) surface with CH₃ adsorbed on the (010) surface to achieve nonoxidative high efficiently C-C coupling with an activation energy of 18.51 kJ/mol. At the same time, this spillover phenomenon inhibits deep dehydrogenation, which is conducive to the selectivity of the C₂ hydrocarbons. The experimental results confirm that the selectivity of the C₂ hydrocarbons is maintained above 99% in the temperature range of 873 K to 1173 K. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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8 pages, 1112 KiB

Open AccessArticle

Probing the Potential Energy Profile of the I + (H₂O)₃ → HI + (H₂O)₂OH Forward and Reverse Reactions: High Level CCSD(T) Studies with Spin-Orbit Coupling Included

by Xinyuan Zhang, Xiaoting Chen, Yan Lin, Yan Meng, Guoliang Li, Yaoming Xie and Henry F. Schaefer III

Molecules 2023, 28(2), 904; https://doi.org/10.3390/molecules28020904 - 16 Jan 2023

Viewed by 1917

Abstract

Three different pathways for the atomic iodine plus water trimer reaction I + (H₂O)₃ → HI + (H₂O)₂OH were preliminarily examined by the DFT-MPW1K method. Related to previous predictions for the F/Cl/Br + (H₂O) [...] Read more.

Three different pathways for the atomic iodine plus water trimer reaction I + (H₂O)₃ → HI + (H₂O)₂OH were preliminarily examined by the DFT-MPW1K method. Related to previous predictions for the F/Cl/Br + (H₂O)₃ reactions, three pathways for the I + (H₂O)₃ reaction are linked in terms of geometry and energetics. To legitimize the results, the “gold standard” CCSD(T) method was employed to investigate the lowest-lying pathway with the correlation-consistent polarized valence basis set up to cc-pVQZ(-PP). According to the CCSD(T)/cc-pVQZ(-PP)//CCSD(T)/cc-pVTZ(-PP) results, the I + (H₂O)₃ → HI + (H₂O)₂OH reaction is predicted to be endothermic by 47.0 kcal mol⁻¹. The submerged transition state is predicted to lie 43.7 kcal mol⁻¹ above the separated reactants. The I···(H₂O)₃ entrance complex lies below the separated reactants by 4.1 kcal mol⁻¹, and spin-orbit coupling has a significant impact on this dissociation energy. The HI···(H₂O)₂OH exit complex is bound by 4.3 kcal mol⁻¹ in relation to the separated products. Compared with simpler I + (H₂O)₂ and I + H₂O reactions, the I + (H₂O)₃ reaction is energetically between them in general. It is speculated that the reaction between the iodine atom and the larger water clusters may be energetically analogous to the I + (H₂O)₃ reaction. The iodine reaction I + (H₂O)₃ is connected with the analogous valence isoelectronic bromine/chlorine reactions Br/Cl + (H₂O)₃ but much different from the F + (H₂O)₃ reaction. Significant difference with other halogen systems, especially for barrier heights, are seen for the iodine systems. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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14 pages, 1991 KiB

Open AccessArticle

Uncertainty Relation and the Thermal Properties of an Isotropic Harmonic Oscillator (IHO) with the Inverse Quadratic (IQ) Potentials and the Pseudo-Harmonic (PH) with the Inverse Quadratic (IQ) Potentials

by Clement A. Onate, Ituen B. Okon, Gian. O. Jude, Michael C. Onyeaju and Akaninyene. D. Antia

Quantum Rep. 2023, 5(1), 38-51; https://doi.org/10.3390/quantum5010004 - 12 Jan 2023

Cited by 2 | Viewed by 1589

Abstract

The solutions for a combination of the isotropic harmonic oscillator plus the inversely quadratic potentials and a combination of the pseudo-harmonic with inversely quadratic potentials has not been reported, though the individual potentials have been given attention. This study focuses on the solutions [...] Read more.

The solutions for a combination of the isotropic harmonic oscillator plus the inversely quadratic potentials and a combination of the pseudo-harmonic with inversely quadratic potentials has not been reported, though the individual potentials have been given attention. This study focuses on the solutions of the combination of the potentials, as stated above using the parametric Nikiforov–Uvarov (PNV) as the traditional technique to obtain the energy equations and their corresponding unnormalized radial wave functions. To deduce the application of these potentials, the expectation values, the uncertainty in the position and momentum, and the thermodynamic properties, such as the mean energy, entropy, heat capacity, and the free mean energy, are also calculated via the partition function. The result shows that the spectra for the PHIQ are higher than the spectra for the IHOIQ. It is also shown that the product of the uncertainties obeyed the Heisenberg uncertainty relation/principle. Finally, the thermal properties of the two potentials exhibit similar behaviours. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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12 pages, 2334 KiB

Open AccessFeature PaperArticle

Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang

by Bella L. Grigorenko, Igor V. Polyakov and Alexander V. Nemukhin

Molecules 2023, 28(2), 505; https://doi.org/10.3390/molecules28020505 - 4 Jan 2023

Cited by 2 | Viewed by 1969

Abstract

We report the results of a computational study of the mechanism of the light-induced chemical reaction of chromophore hydration in the fluorescent protein Dreiklang, responsible for its switching from the fluorescent ON-state to the dark OFF-state. We explore the relief of the charge-transfer [...] Read more.

We report the results of a computational study of the mechanism of the light-induced chemical reaction of chromophore hydration in the fluorescent protein Dreiklang, responsible for its switching from the fluorescent ON-state to the dark OFF-state. We explore the relief of the charge-transfer excited-state potential energy surface in the ON-state to locate minimum energy conical intersection points with the ground-state energy surface. Simulations of the further evolution of model systems allow us to characterize the ground-state reaction intermediate tentatively suggested in the femtosecond studies of the light-induced dynamics in Dreiklang and finally to arrive at the reaction product. The obtained results clarify the details of the photoswitching mechanism in Dreiklang, which is governed by the chemical modification of its chromophore. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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21 pages, 11771 KiB

Open AccessArticle

Conjugative Stabilization versus Anchimeric Assistance in Carbocations

by Bagrat A. Shainyan

Molecules 2023, 28(1), 38; https://doi.org/10.3390/molecules28010038 - 21 Dec 2022

Cited by 1 | Viewed by 1818

Abstract

In this study, an old concept of anchimeric assistance is viewed from a different angle. Primary cations with two different heteroatomic substituents in the α-position to the cationic carbon atom CHXY–CH₂⁺ (X, Y = Me₂N, MeO, Me₃Si, [...] Read more.

In this study, an old concept of anchimeric assistance is viewed from a different angle. Primary cations with two different heteroatomic substituents in the α-position to the cationic carbon atom CHXY–CH₂⁺ (X, Y = Me₂N, MeO, Me₃Si, Me₂P, MeS, MeS, Br) can be stabilized by the migration of either the X or Y group to the cation center. In each case, the migration can be either complete, resulting in the transfer of the migrating group to the adjacent carbon atom and the formation of a secondary carbocation stabilized by the remaining heteroatom, or incomplete, leading to an anchimerically assisted iranium ion. For all combinations of the above groups, these transformations have been studied by theoretical analysis at the MP2/aug-cc-pVTZ level and were shown to occur depending on the ability of anchimeric assistance by X and Y, as well as the conformation of the starting primary carbocation. In the conformers of α-amino cations with the p-orbital, C–N bond and the nitrogen lone pair in one plane, the Me₂N group migrates to the cationic center to give aziranium ions. Otherwise, the second heteroatom is shifted to give iminium ions, without or with very slight anchimeric assistance. In the α-methoxy cations, the MeO group can be shifted to the cationic center to give the O-anchimerically assisted ions as local minima, the global minima being the ions anchimerically assisted by another heteroatom. The electropositive silicon tends to migrate towards the cationic center, but with the formation of a π-complex of the Me₃Si cation with the C=C bond rather than a Si-anchimerically assisted cation. The phosphorus atom can either fully migrate to the cationic center (X = P, Y = S, Se) or form anchimerically stabilized phosphiranium ions (X = P, Y = O, Si, Br). The order of the anchimeric assistance for the heaviest atoms decreases in the order Se >> S > Br. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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13 pages, 2925 KiB

Open AccessArticle

Structural Characteristics, Stability, and Electronic Properties of 001 Surface with Point Defects of Zinc Stannate: A First-Principle Study

by Jun Li, Meilin Zhu, Rou Feng, Yingjie Yuan, Zewei Fu, Liangliang Meng, Yingwu Wang, Ying Zhou, Hui Zhang and Hongcun Bai

Inorganics 2022, 10(12), 258; https://doi.org/10.3390/inorganics10120258 - 13 Dec 2022

Cited by 1 | Viewed by 1653

Abstract

This work presents first-principles calculations on the surface and defect impact upon zinc stannate (ZS) materials with perovskite bulk structures. The structure and electronic properties of both a perfect 001 surface and surfaces with a point defect of ZS were investigated by means [...] Read more.

This work presents first-principles calculations on the surface and defect impact upon zinc stannate (ZS) materials with perovskite bulk structures. The structure and electronic properties of both a perfect 001 surface and surfaces with a point defect of ZS were investigated by means of density functional theory calculations. The cohesive energies of a perfect 001 surface and those with O, Sn, or Zn defects were decreased compared with that of bulk ZS. Oxygen defects on the 001 surface of ZS formed more easily than others based on the obtained cohesive energy and defect formation energy. The electronic properties close to the Fermi levels of bulk ZS materials were mainly controlled by the O 2p and Sn 5s orbitals. The formation of vacancy on the 001 surface of ZS changed the band structure and band gap compared with that of the bulk. The modulation mechanism was explored by means of structure transformation, band structure, and density of states analysis. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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12 pages, 1412 KiB

Open AccessArticle

An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules

by Yanxing Wang, Brandon Duane Walker, Chengwen Liu and Pengyu Ren

Molecules 2022, 27(23), 8567; https://doi.org/10.3390/molecules27238567 - 5 Dec 2022

Cited by 5 | Viewed by 2630

Abstract

Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtained with density functional theory (DFT) methods. However, obtaining a reliable energy profile can [...] Read more.

Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtained with density functional theory (DFT) methods. However, obtaining a reliable energy profile can be time-consuming when the molecular sizes are relatively large or when there are many molecules of interest. Furthermore, incorporation of data-driven deep learning methods into force field development has great requirements for high-quality geometry and energy data. To this end, we compared several possible alternatives to the traditional DFT methods for conformational scans, including the semi-empirical method GFN2-xTB and the neural network potential ANI-2x. It was found that a sequential protocol of geometry optimization with the semi-empirical method and single-point energy calculation with high-level DFT methods can provide satisfactory conformational energy profiles hundreds of times faster in terms of optimization. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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22 pages, 6848 KiB

Open AccessArticle

Tetrel Bonding in Anion Recognition: A First Principles Investigation

by Pradeep R. Varadwaj

Molecules 2022, 27(23), 8449; https://doi.org/10.3390/molecules27238449 - 2 Dec 2022

Cited by 12 | Viewed by 1950

Abstract

Twenty-five molecule–anion complex systems [I₄Tt···X⁻] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability [...] Read more.

Twenty-five molecule–anion complex systems [I₄Tt···X⁻] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability of the tetrel atoms in molecular entities, I₄Tt, to recognize the halide anions when in close proximity. The tetrel bond strength for the [I₄C···X⁻] series and [I₄Tt···X⁻] (Tt = Si, Sn; X = I, At), was weak-to-moderate, whereas that in the remaining 16 complexes was dative tetrel bond type with very large interaction energies and short Tt···X close contact distances. The basis set superposition error corrected interaction energies calculated with the highest-level theory applied, [CCSD(T)/def2-TZVPPD], ranged from −3.0 to −112.2 kcal mol⁻¹. The significant variation in interaction energies was realized as a result of different levels of tetrel bonding environment between the interacting partners at the equilibrium geometries of the complex systems. Although the ωB97X-D computed intermolecular geometries and interaction energies of a majority of the [I₄Tt···X⁻] complexes were close to those predicted by the highest level of theory, the MP2 results were shown to be misleading for some of these systems. To provide insight into the nature of the intermolecular chemical bonding environment in the 25 molecule–anion complexes investigated, we discussed the charge-density-based topological and isosurface features that emanated from the application of the quantum theory of atoms in molecules and independent gradient model approaches, respectively. Full article

(This article belongs to the Topic Theoretical, Quantum and Computational Chemistry)

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