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Chemical Bond and Bonding 2016

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (31 August 2016) | Viewed by 93528

Special Issue Editor

1. Laboratory of Structural and Computational Physical-Chemistry for Nanosciences and QSAR, Biology-Chemistry Department, West University of Timisoara, Str. Pestalozzi 16, 300115 Timisoara, Romania
2. Laboratory of Renewable Energies-Photovoltaics, R&D National Institute for Electrochemistry and Condensed Matter–INCEMC–Timisoara, Str. Dr. Aurel Podeanu 144, 300569 Timișoara, Romania
Interests: quantum physical chemistry; nanochemistry; reactivity indices and principles; electronegativity; density functional theory; path integrals; enzyme kinetics; QSAR; epistemology and philosophy of science
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Special Issue Information

Dear Colleagues,

Chemical Bonding is in the core of Chemistry. It actually defines Chemistry as an autonomous science, with a certain objective to study, understand, and develop; it also opens inter-, multi-, and trans-disciplinary junctions with other mathematical (including informatics), natural (physical and quantum) sciences, and with life (bio, eco, medical, pharma) sciences alike. Nevertheless, the fundamental research on unifying the chemical bonds recognized parallels on a different (and non-reductive) level the Great Unification of Forces in Nature as physics advocates; in this line, a foreseen Physicochemical Grand Unification of Forces would equally be a worthy project for humankind increasing knowledge of existence and betterment of life and of its expanding (given the universal nuclei-synthesis or nuclei-genesis, for instance, in cosmology). On the other side of chemical bond applications, various exotic chemical situations have been reported, such as sextupole bonds, nano- and bio-molecules, and carbon-based aggregates that need both conceptual and computational explanations and experimental analysis. The increased need for molecular design for assessing biotargets through pharmacophores, the practical demands of predictions of acute toxicity of medicines, and environmental waste compounds, all these actual realities of Chemistry, in both its principles and applications, deserve a special forum.

In this generous yet challenging context of the reality and manifesting reality of chemical bonding, the dedicated Topical Collection on “Chemical Bond and Bonding” in an open-access molecular-oriented science forum is both an academic, scholarly, and ultimately a social (including knowledge and economic growth by innovation) contribution to the present for future generations of materials and compounds, while having understood and controlled the chemical bond and interactions in nano- to maco-environments.

The Topical Collection on “Chemical Bond and Bonding” has emerged from earlier Special Issues on this vivid subject for Chemistry and allied molecular sciences, and it will continue the dedicated Special Issue as such.

We kindly invite you to contribute papers, expanding on these and allied concepts, for a scientific understanding and control of chemical bonds for a better life and a sustainable environment in the 21st century.

Kind regards,

Dr. Dr-Habil. Mihai V. Putz
Guest Editor

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Keywords

  • atoms-in-molecules and chemical epistemology
  • bio-chemical and ligand-receptor interaction
  • carbon structures and bonding
  • chemical bonding and nanochemistry
  • chemical graph theory and chemical topology
  • electronegativity and chemical reactivity
  • computational and quantum chemistry
  • crystallography and solid-state chemistry
  • sustainable materials

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Published Papers (14 papers)

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2522 KiB  
Article
Succinimide Formation from an NGR-Containing Cyclic Peptide: Computational Evidence for Catalytic Roles of Phosphate Buffer and the Arginine Side Chain
by Ryota Kirikoshi, Noriyoshi Manabe and Ohgi Takahashi
Int. J. Mol. Sci. 2017, 18(2), 429; https://doi.org/10.3390/ijms18020429 - 16 Feb 2017
Cited by 16 | Viewed by 7240
Abstract
The Asn-Gly-Arg (NGR) motif and its deamidation product isoAsp-Gly-Arg (isoDGR) have recently attracted considerable attention as tumor-targeting ligands. Because an NGR-containing peptide and the corresponding isoDGR-containing peptide target different receptors, the spontaneous NGR deamidation can be used in dual [...] Read more.
The Asn-Gly-Arg (NGR) motif and its deamidation product isoAsp-Gly-Arg (isoDGR) have recently attracted considerable attention as tumor-targeting ligands. Because an NGR-containing peptide and the corresponding isoDGR-containing peptide target different receptors, the spontaneous NGR deamidation can be used in dual targeting strategies. It is well known that the Asn deamidation proceeds via a succinimide derivative. In the present study, we computationally investigated the mechanism of succinimide formation from a cyclic peptide, c[CH2CO-NGRC]-NH2, which has recently been shown to undergo rapid deamidation in a phosphate buffer. An H2PO4 ion was explicitly included in the calculations. We employed the density functional theory using the B3LYP functional. While geometry optimizations were performed in the gas phase, hydration Gibbs energies were calculated by the SM8 (solvation model 8) continuum model. We have found a pathway leading to the five-membered ring tetrahedral intermediate in which both the H2PO4 ion and the Arg side chain act as catalyst. This intermediate, once protonated at the NH2 group on the five-membered ring, was shown to easily undergo NH3 elimination leading to the succinimide formation. This study is the first to propose a possible catalytic role for the Arg side chain in the NGR deamidation. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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2789 KiB  
Article
Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol
by Hailiang Zhao, Shanshan Tang, Xiang Xu and Lin Du
Int. J. Mol. Sci. 2017, 18(1), 4; https://doi.org/10.3390/ijms18010004 - 30 Dec 2016
Cited by 21 | Viewed by 9161
Abstract
Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond [...] Read more.
Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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1641 KiB  
Article
The Thermodynamic and Kinetic Properties of 2-Hydroxypyridine/2-Pyridone Tautomerization: A Theoretical and Computational Revisit
by Safiyah A. Hejazi, Osman I. Osman, Abdulrahman O. Alyoubi, Saadullah G. Aziz and Rifaat H. Hilal
Int. J. Mol. Sci. 2016, 17(11), 1893; https://doi.org/10.3390/ijms17111893 - 14 Nov 2016
Cited by 28 | Viewed by 5501
Abstract
The gas-phase thermal tautomerization reaction between 2-hydroxypyridine (2-HPY) and 2-pyridone (2-PY) was investigated by applying 6-311++G** and aug-cc-pvdz basis sets incorporated into some density functional theory (DFT) and coupled cluster with singles and doubles (CCSD) methods. The geometrical structures, dipole moments, HOMO-LUMO energy [...] Read more.
The gas-phase thermal tautomerization reaction between 2-hydroxypyridine (2-HPY) and 2-pyridone (2-PY) was investigated by applying 6-311++G** and aug-cc-pvdz basis sets incorporated into some density functional theory (DFT) and coupled cluster with singles and doubles (CCSD) methods. The geometrical structures, dipole moments, HOMO-LUMO energy gaps, total hyperpolarizability, kinetics and thermodynamics functions were monitored against the effects of the corrections imposed on these functionals. The small experimental energy difference between the two tautomers of 3.23 kJ/mol; was a real test of the accuracy of the applied levels of theory. M062X and CCSD methods predicted the preference of 2-HPY over 2-PY by 5–9 kJ/mol; while B3LYP functional favoured 2-PY by 1–3 kJ/mol. The CAM-B3LYP and ωB97XD functionals yielded mixed results depending on the basis set used. The source of preference of 2-HPY is the minimal steric hindrance and electrostatic repulsion that subdued the huge hyperconjugation in 2-PY. A 1,3-proton shift intramolecular gas-phase tautomerization yielded a high average activation of 137.152 kJ/mol; while the intermolecular mixed dimer interconversion gave an average barrier height of 30.844 kJ/mol. These findings are boosted by a natural bond orbital (NBO) technique. The low total hyperpolarizabilities of both tautomers mark out their poor nonlinear optical (NLO) behaviour. The enhancement of the total hyperpolarizability of 2-HPY over that of 2-PY is interpreted by the bond length alternation. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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3010 KiB  
Article
Linear Response Function of Bond-Order
by Nayuta Suzuki, Yuki Mitsuta, Mitsutaka Okumura and Shusuke Yamanaka
Int. J. Mol. Sci. 2016, 17(11), 1779; https://doi.org/10.3390/ijms17111779 - 25 Oct 2016
Cited by 1 | Viewed by 4545
Abstract
We present the linear response function of bond-orders (LRF-BO) based on a real space integration scheme for molecular systems. As in the case of the LRF of density, the LRF-BO is defined as the response of the bond order of the molecule for [...] Read more.
We present the linear response function of bond-orders (LRF-BO) based on a real space integration scheme for molecular systems. As in the case of the LRF of density, the LRF-BO is defined as the response of the bond order of the molecule for the virtual perturbation. Our calculations show that the LRF-BO enables us not only to detect inductive and resonating effects of conjugating systems, but also to predict pKa values on substitution groups via linear relationships between the Hammett constants and the LRF-BO values for meta- and para-substituted benzoic acids. More importantly, the LRF-BO values for the O-H bonds strongly depend on the sites to which the virtual perturbation is applied, implying that the LRF-BO values include essential information about reaction mechanism of the acid-dissociation of substituted benzoic acids. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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2319 KiB  
Article
Learning the Relationship between the Primary Structure of HIV Envelope Glycoproteins and Neutralization Activity of Particular Antibodies by Using Artificial Neural Networks
by Cătălin Buiu, Mihai V. Putz and Speranta Avram
Int. J. Mol. Sci. 2016, 17(10), 1710; https://doi.org/10.3390/ijms17101710 - 11 Oct 2016
Cited by 15 | Viewed by 5685
Abstract
The dependency between the primary structure of HIV envelope glycoproteins (ENV) and the neutralization data for given antibodies is very complicated and depends on a large number of factors, such as the binding affinity of a given antibody for a given ENV protein, [...] Read more.
The dependency between the primary structure of HIV envelope glycoproteins (ENV) and the neutralization data for given antibodies is very complicated and depends on a large number of factors, such as the binding affinity of a given antibody for a given ENV protein, and the intrinsic infection kinetics of the viral strain. This paper presents a first approach to learning these dependencies using an artificial feedforward neural network which is trained to learn from experimental data. The results presented here demonstrate that the trained neural network is able to generalize on new viral strains and to predict reliable values of neutralizing activities of given antibodies against HIV-1. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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2133 KiB  
Article
Racemization of the Succinimide Intermediate Formed in Proteins and Peptides: A Computational Study of the Mechanism Catalyzed by Dihydrogen Phosphate Ion
by Ohgi Takahashi, Ryota Kirikoshi and Noriyoshi Manabe
Int. J. Mol. Sci. 2016, 17(10), 1698; https://doi.org/10.3390/ijms17101698 - 10 Oct 2016
Cited by 21 | Viewed by 9355
Abstract
In proteins and peptides, d-aspartic acid (d-Asp) and d-β-Asp residues can be spontaneously formed via racemization of the succinimide intermediate formed from l-Asp and l-asparagine (l-Asn) residues. These biologically uncommon amino acid residues are known [...] Read more.
In proteins and peptides, d-aspartic acid (d-Asp) and d-β-Asp residues can be spontaneously formed via racemization of the succinimide intermediate formed from l-Asp and l-asparagine (l-Asn) residues. These biologically uncommon amino acid residues are known to have relevance to aging and pathologies. Although nonenzymatic, the succinimide racemization will not occur without a catalyst at room or biological temperature. In the present study, we computationally investigated the mechanism of succinimide racemization catalyzed by dihydrogen phosphate ion, H2PO4, by B3LYP/6-31+G(d,p) density functional theory calculations, using a model compound in which an aminosuccinyl (Asu) residue is capped with acetyl (Ace) and NCH3 (Nme) groups on the N- and C-termini, respectively (Ace–Asu–Nme). It was shown that an H2PO4 ion can catalyze the enolization of the Hα–Cα–C=O portion of the Asu residue by acting as a proton-transfer mediator. The resulting complex between the enol form and H2PO4 corresponds to a very flat intermediate region on the potential energy surface lying between the initial reactant complex and its mirror-image geometry. The calculated activation barrier (18.8 kcal·mol−1 after corrections for the zero-point energy and the Gibbs energy of hydration) for the enolization was consistent with the experimental activation energies of Asp racemization. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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2717 KiB  
Article
Construction of Metabolism Prediction Models for CYP450 3A4, 2D6, and 2C9 Based on Microsomal Metabolic Reaction System
by Shuai-Bing He, Man-Man Li, Bai-Xia Zhang, Xiao-Tong Ye, Ran-Feng Du, Yun Wang and Yan-Jiang Qiao
Int. J. Mol. Sci. 2016, 17(10), 1686; https://doi.org/10.3390/ijms17101686 - 09 Oct 2016
Cited by 7 | Viewed by 6154
Abstract
During the past decades, there have been continuous attempts in the prediction of metabolism mediated by cytochrome P450s (CYP450s) 3A4, 2D6, and 2C9. However, it has indeed remained a huge challenge to accurately predict the metabolism of xenobiotics mediated by these enzymes. To [...] Read more.
During the past decades, there have been continuous attempts in the prediction of metabolism mediated by cytochrome P450s (CYP450s) 3A4, 2D6, and 2C9. However, it has indeed remained a huge challenge to accurately predict the metabolism of xenobiotics mediated by these enzymes. To address this issue, microsomal metabolic reaction system (MMRS)—a novel concept, which integrates information about site of metabolism (SOM) and enzyme—was introduced. By incorporating the use of multiple feature selection (FS) techniques (ChiSquared (CHI), InfoGain (IG), GainRatio (GR), Relief) and hybrid classification procedures (Kstar, Bayes (BN), K-nearest neighbours (IBK), C4.5 decision tree (J48), RandomForest (RF), Support vector machines (SVM), AdaBoostM1, Bagging), metabolism prediction models were established based on metabolism data released by Sheridan et al. Four major biotransformations, including aliphatic C-hydroxylation, aromatic C-hydroxylation, N-dealkylation and O-dealkylation, were involved. For validation, the overall accuracies of all four biotransformations exceeded 0.95. For receiver operating characteristic (ROC) analysis, each of these models gave a significant area under curve (AUC) value >0.98. In addition, an external test was performed based on dataset published previously. As a result, 87.7% of the potential SOMs were correctly identified by our four models. In summary, four MMRS-based models were established, which can be used to predict the metabolism mediated by CYP3A4, 2D6, and 2C9 with high accuracy. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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1491 KiB  
Communication
(Salen)Mn(III) Catalyzed Asymmetric Epoxidation Reactions by Hydrogen Peroxide in Water: A Green Protocol
by Francesco Paolo Ballistreri, Chiara M. A. Gangemi, Andrea Pappalardo, Gaetano A. Tomaselli, Rosa Maria Toscano and Giuseppe Trusso Sfrazzetto
Int. J. Mol. Sci. 2016, 17(7), 1112; https://doi.org/10.3390/ijms17071112 - 12 Jul 2016
Cited by 28 | Viewed by 6126
Abstract
Enantioselective epoxidation reactions of some chosen reactive alkenes by a chiral Mn(III) salen catalyst were performed in H2O employing H2O2 as oxidant and diethyltetradecylamine N-oxide (AOE-14) as surfactant. This procedure represents an environmentally benign protocol which leads [...] Read more.
Enantioselective epoxidation reactions of some chosen reactive alkenes by a chiral Mn(III) salen catalyst were performed in H2O employing H2O2 as oxidant and diethyltetradecylamine N-oxide (AOE-14) as surfactant. This procedure represents an environmentally benign protocol which leads to e.e. values ranging from good to excellent (up to 95%). Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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411 KiB  
Article
Replacement of Oxygen by Sulfur in Small Organic Molecules. 3. Theoretical Studies on the Tautomeric Equilibria of the 2OH and 4OH-Substituted Oxazole and Thiazole and the 3OH and 4OH-Substituted Isoxazole and Isothiazole in the Isolated State and in Solution
by Peter I. Nagy
Int. J. Mol. Sci. 2016, 17(7), 1094; https://doi.org/10.3390/ijms17071094 - 09 Jul 2016
Cited by 4 | Viewed by 5895
Abstract
This follow-up paper completes the author’s investigations to explore the in-solution structural preferences and relative free energies of all OH-substituted oxazole, thiazole, isoxazole, and isothiazole systems. The polarizable continuum dielectric solvent method calculations in the integral-equation formalism (IEF-PCM) were performed at the DFT/B97D/aug-cc-pv(q+(d))z [...] Read more.
This follow-up paper completes the author’s investigations to explore the in-solution structural preferences and relative free energies of all OH-substituted oxazole, thiazole, isoxazole, and isothiazole systems. The polarizable continuum dielectric solvent method calculations in the integral-equation formalism (IEF-PCM) were performed at the DFT/B97D/aug-cc-pv(q+(d))z level for the stable neutral tautomers with geometries optimized in dichloromethane and aqueous solution. With the exception of the predictions for the predominant tautomers of the 3OH isoxazole and isothiazole, the results of the IEF-PCM calculations for identifying the most stable tautomer of the given species in the two selected solvents agreed with those from experimental investigations. The calculations predict that the hydroxy proton, with the exception for the 4OH isoxazole and 4OH isothiazole, moves preferentially to the ring nitrogen or to a ring carbon atom in parallel with the development of a C=O group. The remaining, low-fraction OH tautomers will not be observable in the equilibrium compositions. Relative solvation free energies obtained by the free energy perturbation method implemented in Monte Carlo simulations are in moderate accord with the IEF-PCM results, but consideration of the ΔGsolv/MC values in calculating ΔGstot maintains the tautomeric preferences. It was revealed from the Monte Carlo solution structure analyses that the S atom is not a hydrogen-bond acceptor in any OH-substituted thiazole or isothiazole, and the OH-substituted isoxazole and oxazole ring oxygens may act as a weak hydrogen-bond acceptor at most. The molecules form 1.0−3.4 solute−water hydrogen bonds in generally unexplored numbers at some specific solute sites. Nonetheless, hydrogen-bond formation is favorable with the NH, C=O and OH groups. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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3747 KiB  
Article
Protonation Sites, Tandem Mass Spectrometry and Computational Calculations of o-Carbonyl Carbazolequinone Derivatives
by Maximiliano Martínez-Cifuentes, Graciela Clavijo-Allancan, Pamela Zuñiga-Hormazabal, Braulio Aranda, Andrés Barriga, Boris Weiss-López and Ramiro Araya-Maturana
Int. J. Mol. Sci. 2016, 17(7), 1071; https://doi.org/10.3390/ijms17071071 - 05 Jul 2016
Cited by 4 | Viewed by 5610
Abstract
A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical [...] Read more.
A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical parameters such as molecular electrostatic potential (MEP), local Fukui functions and local Parr function for electrophilic attack as well as proton affinity (PA) and gas phase basicity (GB), were used to explain the preferred protonation sites. Transition states of some main fragmentation routes were obtained and the energies calculated at density functional theory (DFT) B3LYP level were compared with the obtained by ab initio quadratic configuration interaction with single and double excitation (QCISD). The results are in accordance with the observed distribution of ions. The nature of the substituents in the aromatic ring has a notable impact on the fragmentation routes of the molecules. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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3150 KiB  
Article
Linear and Branched PEIs (Polyethylenimines) and Their Property Space
by Claudiu N. Lungu, Mircea V. Diudea, Mihai V. Putz and Ireneusz P. Grudziński
Int. J. Mol. Sci. 2016, 17(4), 555; https://doi.org/10.3390/ijms17040555 - 13 Apr 2016
Cited by 49 | Viewed by 7139
Abstract
A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical [...] Read more.
A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical) properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship) studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent) and is reflected in its local electronic (and/or magnetic) properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI) macromolecules (linear LPEI and branched BPEI, respectively) with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting) energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry) purpose. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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3619 KiB  
Article
Exploring the Interaction Natures in Plutonyl (VI) Complexes with Topological Analyses of Electron Density
by Jiguang Du, Xiyuan Sun and Gang Jiang
Int. J. Mol. Sci. 2016, 17(4), 414; https://doi.org/10.3390/ijms17040414 - 11 Apr 2016
Cited by 12 | Viewed by 5495
Abstract
The interaction natures between Pu and different ligands in several plutonyl (VI) complexes are investigated by performing topological analyses of electron density. The geometrical structures in both gaseous and aqueous phases are obtained with B3LYP functional, and are generally in agreement with available [...] Read more.
The interaction natures between Pu and different ligands in several plutonyl (VI) complexes are investigated by performing topological analyses of electron density. The geometrical structures in both gaseous and aqueous phases are obtained with B3LYP functional, and are generally in agreement with available theoretical and experimental results when combined with all-electron segmented all-electron relativistic contracted (SARC) basis set. The Pu– O y l bond orders show significant linear dependence on bond length and the charge of oxygen atoms in plutonyl moiety. The closed-shell interactions were identified for Pu-Ligand bonds in most complexes with quantum theory of atoms in molecules (QTAIM) analyses. Meanwhile, we found that some Pu–Ligand bonds, like Pu–OH, show weak covalent. The interactive nature of Pu–ligand bonds were revealed based on the interaction quantum atom (IQA) energy decomposition approach, and our results indicate that all Pu–Ligand interactions is dominated by the electrostatic attraction interaction as expected. Meanwhile it is also important to note that the quantum mechanical exchange-correlation contributions can not be ignored. By means of the non-covalent interaction (NCI) approach it has been found that some weak and repulsion interactions existed in plutonyl(VI) complexes, which can not be distinguished by QTAIM, can be successfully identified. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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1999 KiB  
Article
Optical Absorption Spectra and Electronic Properties of Symmetric and Asymmetric Squaraine Dyes for Use in DSSC Solar Cells: DFT and TD-DFT Studies
by Reda M. El-Shishtawy, Shaaban A. Elroby, Abdullah M. Asiri and Klaus Müllen
Int. J. Mol. Sci. 2016, 17(4), 487; https://doi.org/10.3390/ijms17040487 - 01 Apr 2016
Cited by 27 | Viewed by 7800
Abstract
The electronic absorption spectra, ground-state geometries and electronic structures of symmetric and asymmetric squaraine dyes (SQD1–SQD4) were investigated using density functional theory (DFT) and time-dependent (TD-DFT) density functional theory at the B3LYP/6-311++G** level. The calculated ground-state geometries reveal pronounced conjugation in these dyes. [...] Read more.
The electronic absorption spectra, ground-state geometries and electronic structures of symmetric and asymmetric squaraine dyes (SQD1–SQD4) were investigated using density functional theory (DFT) and time-dependent (TD-DFT) density functional theory at the B3LYP/6-311++G** level. The calculated ground-state geometries reveal pronounced conjugation in these dyes. Long-range corrected time dependent density functionals Perdew, Burke and Ernzerhof (PBE, PBE1PBE (PBE0)), and the exchange functional of Tao, Perdew, Staroverov, and Scuseria (TPSSh) with 6-311++G** basis set were employed to examine optical absorption properties. In an extensive comparison between the optical data and DFT benchmark calculations, the BEP functional with 6-311++G** basis set was found to be the most appropriate in describing the electronic absorption spectra. The calculated energy values of lowest unoccupied molecular orbitals (LUMO) were 3.41, 3.19, 3.38 and 3.23 eV for SQD1, SQD2, SQD3, and SQD4, respectively. These values lie above the LUMO energy (−4.26 eV) of the conduction band of TiO2 nanoparticles indicating possible electron injection from the excited dyes to the conduction band of the TiO2 in dye-sensitized solar cells (DSSCs). Also, aromaticity computation for these dyes are in good agreement with the data obtained optically and geometrically with SQD4 as the highest aromatic structure. Based on the optimized molecular geometries, relative positions of the frontier orbitals, and the absorption maxima, we propose that these dyes are suitable components of photovoltaic DSSC devices. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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1417 KiB  
Letter
The Chlorophyll a Fluorescence Modulated by All-Trans-β-Carotene in the Process of Photosystem II
by Tianyu Li, Ye Zhang, Nan Gong, Zuowei Li, Chenglin Sun and Zhiwei Men
Int. J. Mol. Sci. 2016, 17(6), 978; https://doi.org/10.3390/ijms17060978 - 21 Jun 2016
Cited by 7 | Viewed by 6940
Abstract
Modulating the chlorophyll a (Chl-a) fluorescence by all-trans-β-Carotene (β-Car) in the polarity and non-polarity solutions was investigated. The fluorescence intensity of Chl-a decreased as the concentration of β-Car increased. The excited electronic levels of Chl-a and β-Car became much closer owing to the [...] Read more.
Modulating the chlorophyll a (Chl-a) fluorescence by all-trans-β-Carotene (β-Car) in the polarity and non-polarity solutions was investigated. The fluorescence intensity of Chl-a decreased as the concentration of β-Car increased. The excited electronic levels of Chl-a and β-Car became much closer owing to the solvent effect, which led to the electron transfer between both two molecules. A electron-separated pair Chl·Chl+ that is not luminous was formed due to electron transfer. The solution of Chl-a and β-car in C3H6O was similar to the internal environment of chloroplast. We conclude that the polar solvent is good for the fluorescent modulation in photosystem II. Full article
(This article belongs to the Special Issue Chemical Bond and Bonding 2016)
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