International Journal of Molecular Sciences

2017

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2522 KiB

Open AccessArticle

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 7816

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

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1297 KiB

Open AccessArticle

DFT Study of the Structure, Reactivity, Natural Bond Orbital and Hyperpolarizability of Thiazole Azo Dyes

by Osman I. Osman

Int. J. Mol. Sci. 2017, 18(2), 239; https://doi.org/10.3390/ijms18020239 - 1 Feb 2017

Cited by 34 | Viewed by 7034

Abstract

The structure, reactivity, natural bond orbital (NBO), linear and nonlinear optical (NLO) properties of three thiazole azo dyes (A, B and C) were monitored by applying B3LYP, CAM-B3LYP and ωB97XD functionals with 6-311++G** and aug-cc-pvdz basis sets. The geometrical parameters,dipolemoments,HOMO-LUMO(highest occupied molecular orbital,lowest [...] Read more.

The structure, reactivity, natural bond orbital (NBO), linear and nonlinear optical (NLO) properties of three thiazole azo dyes (A, B and C) were monitored by applying B3LYP, CAM-B3LYP and ωB97XD functionals with 6-311++G** and aug-cc-pvdz basis sets. The geometrical parameters,dipolemoments,HOMO-LUMO(highest occupied molecular orbital,lowest unoccupied molecular orbital) energy gaps, absorption wavelengths and total hyperpolarizabilities were investigated in carbon tetrachloride (CCl4) chloroform (CHCl3), dichloromethane (CH2Cl2) and dimethlysulphoxide (DMSO). The donor methoxyphenyl group deviates from planarity with the thiazole azo moiety by ca. 38◦; while the acceptor dicyanovinyl, indandione and dicyanovinylindanone groups diverge by ca. 6◦. The HOMOs for the three dyes are identical. They spread over the methoxyphenyl donor moiety, the thiazole and benzene rings as π-bonding orbitals. The LUMOs are shaped up by the nature of the acceptor moieties. The LUMOs of the A, B and C dyes extend over the indandione, malononitrile and dicyanovinylindanone acceptor moieties, respectively, as π-antibonding orbitals. The HOMO-LUMO splittings showed that Dye C is much more reactive than dyes A and B. Compared to dyes A and B, Dye C yielded a longer maximum absorption wavelength because of the stabilization of its LUMOs relative to those of the other two. The three dyes show solvatochromism accompanied by signiﬁcant increases in hyperpolarizability. The enhancement of the total hyperpolarizability of C compared to those of A and B is due to the cumulative action of the long π-conjugation of the indanone ring and the stronger electron-withdrawing ability of the dicyanovinyl moiety that form the dicyanovinylindanone acceptor group. These ﬁndings are facilitated by a natural bond orbital (NBO) technique. The very high total hyperpolarizabilities of the three dyes deﬁne their potent nonlinear optical (NLO) behaviour. Full article

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2016

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2789 KiB

Open AccessArticle

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 25 | Viewed by 10038

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

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Open AccessArticle

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 29 | Viewed by 6073

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

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3010 KiB

Open AccessArticle

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 4874

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 pK_a 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

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2319 KiB

Open AccessArticle

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 16 | Viewed by 6022

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

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2133 KiB

Open AccessArticle

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 25 | Viewed by 9939

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 H_α–C_α–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

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2717 KiB

Open AccessArticle

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 - 9 Oct 2016

Cited by 11 | Viewed by 6560

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

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1491 KiB

Open AccessCommunication

(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 29 | Viewed by 6611

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

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411 KiB

Open AccessArticle

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 - 9 Jul 2016

Cited by 5 | Viewed by 6338

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 ΔG_solv/MC values in calculating ΔG^s_tot 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

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3747 KiB

Open AccessArticle

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 - 5 Jul 2016

Cited by 4 | Viewed by 6060

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

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1417 KiB

Open AccessLetter

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 8 | Viewed by 7453

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

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3150 KiB

Open AccessArticle

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 56 | Viewed by 8019

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

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3619 KiB

Open AccessArticle

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 13 | Viewed by 5863

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

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1999 KiB

Open AccessArticle

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 - 1 Apr 2016

Cited by 30 | Viewed by 8413

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

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2015

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3580 KiB

Open AccessArticle

Insight into the Structural Determinants of Imidazole Scaffold-Based Derivatives as TNF-α Release Inhibitors by in Silico Explorations

by Yuan Wang, Mingwei Wu, Chunzhi Ai and Yonghua Wang

Int. J. Mol. Sci. 2015, 16(9), 20118-20138; https://doi.org/10.3390/ijms160920118 - 25 Aug 2015

Cited by 5 | Viewed by 5366

Abstract

Presently, 151 widely-diverse pyridinylimidazole-based compounds that show inhibitory activities at the TNF-α release were investigated. By using the distance comparison technique (DISCOtech), comparative molecular field analysis (CoMFA), and comparative molecular similarity index analysis (CoMSIA) methods, the pharmacophore models and the three-dimensional quantitative structure-activity [...] Read more.

Presently, 151 widely-diverse pyridinylimidazole-based compounds that show inhibitory activities at the TNF-α release were investigated. By using the distance comparison technique (DISCOtech), comparative molecular field analysis (CoMFA), and comparative molecular similarity index analysis (CoMSIA) methods, the pharmacophore models and the three-dimensional quantitative structure-activity relationships (3D-QSAR) of the compounds were explored. The proposed pharmacophore model, including two hydrophobic sites, two aromatic centers, two H-bond donor atoms, two H-bond acceptor atoms, and two H-bond donor sites characterizes the necessary structural features of TNF-α release inhibitors. Both the resultant CoMFA and CoMSIA models exhibited satisfactory predictability (with Q² (cross-validated correlation coefficient) = 0.557, R²_ncv (non-cross-validated correlation coefficient) = 0.740, R²_pre (predicted correlation coefficient) = 0.749 and Q² = 0.598, R²_ncv = 0.767, R²_pre = 0.860, respectively). Good consistency was observed between the 3D-QSAR models and the pharmacophore model that the hydrophobic interaction and hydrogen bonds play crucial roles in the mechanism of actions. The corresponding contour maps generated by these models provide more diverse information about the key intermolecular interactions of inhibitors with the surrounding environment. All these models have extended the understanding of imidazole-based compounds in the structure-activity relationship, and are useful for rational design and screening of novel 2-thioimidazole-based TNF-α release inhibitors. Full article

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4364 KiB

Open AccessArticle

Double Variational Binding—(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands

by Mihai V. Putz, Nicoleta A. Dudaș and Adriana Isvoran

Int. J. Mol. Sci. 2015, 16(8), 19553-19601; https://doi.org/10.3390/ijms160819553 - 18 Aug 2015

Cited by 8 | Viewed by 7464

Abstract

Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed [...] Read more.

Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process. Full article

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Open AccessArticle

Formation of Chlorotriophenoxy Radicals from Complete Series Reactions of Chlorotriophenols with H and OH Radicals

by Fei Xu, Xiangli Shi, Qingzhu Zhang and Wenxing Wang

Int. J. Mol. Sci. 2015, 16(8), 18714-18731; https://doi.org/10.3390/ijms160818714 - 11 Aug 2015

Cited by 11 | Viewed by 5177

Abstract

The chlorothiophenoxy radicals (CTPRs) are key intermediate species in the formation of polychlorinated dibenzothiophenes/thianthrenes (PCDT/TAs). In this work, the formation of CTPRs from the complete series reactions of 19 chlorothiophenol (CTP) congeners with H and OH radicals were investigated theoretically by using the [...] Read more.

The chlorothiophenoxy radicals (CTPRs) are key intermediate species in the formation of polychlorinated dibenzothiophenes/thianthrenes (PCDT/TAs). In this work, the formation of CTPRs from the complete series reactions of 19 chlorothiophenol (CTP) congeners with H and OH radicals were investigated theoretically by using the density functional theory (DFT) method. The profiles of the potential energy surface were constructed at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. The rate constants were evaluated by the canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) contribution at 600–1200 K. The present study indicates that the structural parameters, thermal data, and rate constants as well as the formation potential of CTPRs from CTPs are strongly dominated by the chlorine substitution at the ortho-position of CTPs. Comparison with the study of formation of chlorophenoxy radicals (CPRs) from chlorophenols (CPs) clearly shows that the thiophenoxyl-hydrogen abstraction from CTPs by H is more efficient than the phenoxyl-hydrogen abstraction from CPs by H, whereas the thiophenoxyl-hydrogen abstraction from CTPs by OH is less impactful than the phenoxyl-hydrogen abstraction from CPs by OH. Reactions of CTPs with H can occur more readily than that of CTPs with OH, which is opposite to the reactivity comparison of CPs with H and OH. Full article

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Open AccessArticle

A Combined Pharmacophore Modeling, 3D QSAR and Virtual Screening Studies on Imidazopyridines as B-Raf Inhibitors

by Huiding Xie, Lijun Chen, Jianqiang Zhang, Xiaoguang Xie, Kaixiong Qiu and Jijun Fu

Int. J. Mol. Sci. 2015, 16(6), 12307-12323; https://doi.org/10.3390/ijms160612307 - 29 May 2015

Cited by 24 | Viewed by 6525

Abstract

B-Raf kinase is an important target in treatment of cancers. In order to design and find potent B-Raf inhibitors (BRIs), 3D pharmacophore models were created using the Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database (GALAHAD). The best pharmacophore model obtained [...] Read more.

B-Raf kinase is an important target in treatment of cancers. In order to design and find potent B-Raf inhibitors (BRIs), 3D pharmacophore models were created using the Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database (GALAHAD). The best pharmacophore model obtained which was used in effective alignment of the data set contains two acceptor atoms, three donor atoms and three hydrophobes. In succession, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on 39 imidazopyridine BRIs to build three dimensional quantitative structure-activity relationship (3D QSAR) models based on both pharmacophore and docking alignments. The CoMSIA model based on the pharmacophore alignment shows the best result (q² = 0.621, r²_pred = 0.885). This 3D QSAR approach provides significant insights that are useful for designing potent BRIs. In addition, the obtained best pharmacophore model was used for virtual screening against the NCI2000 database. The hit compounds were further filtered with molecular docking, and their biological activities were predicted using the CoMSIA model, and three potential BRIs with new skeletons were obtained. Full article

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Open AccessShort Note

Acetic Acid-Catalyzed Formation of N-Phenylphthalimide from Phthalanilic Acid: A Computational Study of the Mechanism

by Ohgi Takahashi, Ryota Kirikoshi and Noriyoshi Manabe

Int. J. Mol. Sci. 2015, 16(6), 12174-12184; https://doi.org/10.3390/ijms160612174 - 28 May 2015

Cited by 5 | Viewed by 7582

Abstract

In glacial acetic acid, phthalanilic acid and its monosubstituents are known to be converted to the corresponding phthalimides in relatively good yields. In this study, we computationally investigated the experimentally proposed two-step (addition-elimination or cyclization-dehydration) mechanism at the second-order Møller-Plesset perturbation (MP2) level [...] Read more.

In glacial acetic acid, phthalanilic acid and its monosubstituents are known to be converted to the corresponding phthalimides in relatively good yields. In this study, we computationally investigated the experimentally proposed two-step (addition-elimination or cyclization-dehydration) mechanism at the second-order Møller-Plesset perturbation (MP2) level of theory for the unsubstituted phthalanilic acid, with an explicit acetic acid molecule included in the calculations. In the first step, a gem-diol tetrahedral intermediate is formed by the nucleophilic attack of the amide nitrogen. The second step is dehydration of the intermediate to give N-phenylphthalimide. In agreement with experimental findings, the second step has been shown to be rate-determining. Most importantly, both of the steps are catalyzed by an acetic acid molecule, which acts both as proton donor and acceptor. The present findings, along with those from our previous studies, suggest that acetic acid and other carboxylic acids (in their undissociated forms) can catalyze intramolecular nucleophilic attacks by amide nitrogens and breakdown of the resulting tetrahedral intermediates, acting simultaneously as proton donor and acceptor. In other words, double proton transfers involving a carboxylic acid molecule can be part of an extensive bond reorganization process from cyclic hydrogen-bonded complexes. Full article

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Open AccessArticle

Crystal Structure, Chemical Bonding and Magnetism Studies for Three Quinary Polar Intermetallic Compounds in the (Eu_1−xCa_x)₉In₈(Ge_1−ySn_y)₈ (x = 0.66, y = 0.03) and the (Eu_1−xCa_x)₃In(Ge_3−ySn_1+y) (x = 0.66, 0.68; y = 0.13, 0.27) Phases

by Hyein Woo, Eunyoung Jang, Jin Kim, Yunho Lee, Jongsik Kim and Tae-Soo You

Int. J. Mol. Sci. 2015, 16(4), 9017-9036; https://doi.org/10.3390/ijms16049017 - 22 Apr 2015

Cited by 14 | Viewed by 6839

Abstract

Three quinary polar intermetallic compounds in the (Eu_1−xCa_x)₉In₈(Ge_1−ySn_y)₈ (x = 0.66, y = 0.03) and the (Eu_1−xCa_x)₃In(Ge_3-ySn [...] Read more.

Three quinary polar intermetallic compounds in the (Eu_1−xCa_x)₉In₈(Ge_1−ySn_y)₈ (x = 0.66, y = 0.03) and the (Eu_1−xCa_x)₃In(Ge_3-ySn_1+y) (x = 0.66, 0.68; y = 0.13, 0.27) phases have been synthesized using the molten In-metal flux method, and the crystal structures are characterized by powder and single-crystal X-ray diffractions. Two orthorhombic structural types can be viewed as an assembly of polyanionic frameworks consisting of the In(Ge/Sn)₄ tetrahedral chains, the bridging Ge₂ dimers, either the annulene-like “12-membered rings” for the (Eu_1−xCa_x)₉In₈(Ge_1−ySn_y)₈ series or the cis-trans Ge/Sn-chains for the (Eu_1−xCa_x)₃In(Ge_3−ySn_1+y) series, and several Eu/Ca-mixed cations. The most noticeable difference between two structural types is the amount and the location of the Sn-substitution for Ge: only a partial substitution (11%) occurs at the In(Ge/Sn)₄ tetrahedron in the (Eu_1−xCa_x)₉In₈(Ge_1−ySn_y)₈ series, whereas both a complete and a partial substitution (up to 27%) are observed, respectively, at the cis-trans Ge/Sn-chain and at the In(Ge/Sn)₄ tetrahedron in the (Eu_1−xCa_x)₃In(Ge_3−ySn_1+y) series. A series of tight-binding linear muffin-tin orbital calculations is conducted to understand overall electronic structures and chemical bonding among components. Magnetic susceptibility measurement indicates a ferromagnetic ordering of Eu atoms below 5 K for Eu_1.02(1)Ca_1.98InGe_2.87(1)Sn_1.13. Full article

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Open AccessArticle

Chemical Bonding: The Orthogonal Valence-Bond View

by Alexander F. Sax

Int. J. Mol. Sci. 2015, 16(4), 8896-8933; https://doi.org/10.3390/ijms16048896 - 21 Apr 2015

Cited by 4 | Viewed by 6855

Abstract

Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF) wave functions, these processes can [...] Read more.

Chemical bonding is the stabilization of a molecular system by charge- and spin-reorganization processes in chemical reactions. These processes are said to be local, because the number of atoms involved is very small. With multi-configurational self-consistent field (MCSCF) wave functions, these processes can be calculated, but the local information is hidden by the delocalized molecular orbitals (MO) used to construct the wave functions. The transformation of such wave functions into valence bond (VB) wave functions, which are based on localized orbitals, reveals the hidden information; this transformation is called a VB reading of MCSCF wave functions. The two-electron VB wave functions describing the Lewis electron pair that connects two atoms are frequently called covalent or neutral, suggesting that these wave functions describe an electronic situation where two electrons are never located at the same atom; such electronic situations and the wave functions describing them are called ionic. When the distance between two atoms decreases, however, every covalent VB wave function composed of non-orthogonal atomic orbitals changes its character from neutral to ionic. However, this change in the character of conventional VB wave functions is hidden by its mathematical form. Orthogonal VB wave functions composed of orthonormalized orbitals never change their character. When localized fragment orbitals are used instead of atomic orbitals, one can decide which local information is revealed and which remains hidden. In this paper, we analyze four chemical reactions by transforming the MCSCF wave functions into orthogonal VB wave functions; we show how the reactions are influenced by changing the atoms involved or by changing their local symmetry. Using orthogonal instead of non-orthogonal orbitals is not just a technical issue; it also changes the interpretation, revealing the properties of wave functions that remain otherwise undetected. Full article

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Open AccessArticle

Decisive Interactions between the Heterocyclic Moiety and the Cluster Observed in Polyoxometalate-Surfactant Hybrid Crystals

by Saki Otobe, Natsumi Fujioka, Takuro Hirano, Eri Ishikawa, Haruo Naruke, Katsuhiko Fujio and Takeru Ito

Int. J. Mol. Sci. 2015, 16(4), 8505-8516; https://doi.org/10.3390/ijms16048505 - 16 Apr 2015

Cited by 6 | Viewed by 5546

Abstract

Inorganic-organic hybrid crystals were successfully obtained as single crystals by using polyoxotungstate anion and cationic dodecylpyridazinium (C₁₂pda) and dodecylpyridinium (C₁₂py) surfactants. The decatungstate (W₁₀) anion was used as the inorganic component, and the crystal structures were compared. [...] Read more.

Inorganic-organic hybrid crystals were successfully obtained as single crystals by using polyoxotungstate anion and cationic dodecylpyridazinium (C₁₂pda) and dodecylpyridinium (C₁₂py) surfactants. The decatungstate (W₁₀) anion was used as the inorganic component, and the crystal structures were compared. In the crystal comprising C₁₂pda (C₁₂pda-W₁₀), the heterocyclic moiety directly interacted with W₁₀, which contributed to a build-up of the crystal structure. On the other hand, the crystal consisting of C₁₂py (C₁₂py-W₁₀) had similar crystal packing and molecular arrangement to those in the W₁₀ crystal hybridized with other pyridinium surfactants. These results indicate the significance of the heterocyclic moiety of the surfactant to construct hybrid crystals with polyoxometalate anions. Full article

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Open AccessArticle

From ELF to Compressibility in Solids

by Julia Contreras-García, Miriam Marqués, José Manuel Menéndez and José Manuel Recio

Int. J. Mol. Sci. 2015, 16(4), 8151-8167; https://doi.org/10.3390/ijms16048151 - 13 Apr 2015

Cited by 10 | Viewed by 6082

Abstract

Understanding the electronic nature of materials’ compressibility has alwaysbeen a major issue behind tabulation and rationalization of bulk moduli. This is especiallybecause this understanding is one of the main approaches to the design and proposal of newmaterials with a desired (e.g., ultralow) compressibility. [...] Read more.

Understanding the electronic nature of materials’ compressibility has alwaysbeen a major issue behind tabulation and rationalization of bulk moduli. This is especiallybecause this understanding is one of the main approaches to the design and proposal of newmaterials with a desired (e.g., ultralow) compressibility. It is well recognized that the softestpart of the solid will be the one responsible for its compression at the first place. In chemicalterms, this means that the valence will suffer the main consequences of pressurization.It is desirable to understand this response to pressure in terms of the valence properties(charge, volume, etc.). One of the possible approaches is to consider models of electronicseparability, such as the bond charge model (BCM), which provides insight into the cohesionof covalent crystals in analogy with the classical ionic model. However, this model relies onempirical parametrization of bond and lone pair properties. In this contribution, we havecoupled electron localization function (ELF) ab initio data with the bond charge modeldeveloped by Parr in order to analyze solid state compressibility from first principles andmoreover, to derive general trends and shed light upon superhard behavior. Full article

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Open AccessArticle

Glycolic Acid-Catalyzed Deamidation of Asparagine Residues in Degrading PLGA Matrices: A Computational Study

by Noriyoshi Manabe, Ryota Kirikoshi and Ohgi Takahashi

Int. J. Mol. Sci. 2015, 16(4), 7261-7272; https://doi.org/10.3390/ijms16047261 - 31 Mar 2015

Cited by 10 | Viewed by 6543

Abstract

Poly(lactic-co-glycolic acid) (PLGA) is a strong candidate for being a drug carrier in drug delivery systems because of its biocompatibility and biodegradability. However, in degrading PLGA matrices, the encapsulated peptide and protein drugs can undergo various degradation reactions, including deamidation at [...] Read more.

Poly(lactic-co-glycolic acid) (PLGA) is a strong candidate for being a drug carrier in drug delivery systems because of its biocompatibility and biodegradability. However, in degrading PLGA matrices, the encapsulated peptide and protein drugs can undergo various degradation reactions, including deamidation at asparagine (Asn) residues to give a succinimide species, which may affect their potency and/or safety. Here, we show computationally that glycolic acid (GA) in its undissociated form, which can exist in high concentration in degrading PLGA matrices, can catalyze the succinimide formation from Asn residues by acting as a proton-transfer mediator. A two-step mechanism was studied by quantum-chemical calculations using Ace-Asn-Nme (Ace = acetyl, Nme = NHCH₃) as a model compound. The first step is cyclization (intramolecular addition) to form a tetrahedral intermediate, and the second step is elimination of ammonia from the intermediate. Both steps involve an extensive bond reorganization mediated by a GA molecule, and the first step was predicted to be rate-determining. The present findings are expected to be useful in the design of more effective and safe PLGA devices. Full article

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Open AccessArticle

Towards Understanding the Decomposition/Isomerism Channels of Stratospheric Bromine Species: Ab Initio and Quantum Topology Study

by Saadullah G. Aziz, Abdulrahman O. Alyoubi, Shaaban A. Elroby, Osman I. Osman and Rifaat H. Hilal

Int. J. Mol. Sci. 2015, 16(4), 6783-6800; https://doi.org/10.3390/ijms16046783 - 25 Mar 2015

Cited by 7 | Viewed by 6100

Abstract

The present study aims at a fundamental understanding of bonding characteristics of the C–Br and O–Br bonds. The target molecular systems are the isomeric CH₃OBr/BrCH₂OH system and their decomposition products. Calculations of geometries and frequencies at different density functional [...] Read more.

The present study aims at a fundamental understanding of bonding characteristics of the C–Br and O–Br bonds. The target molecular systems are the isomeric CH₃OBr/BrCH₂OH system and their decomposition products. Calculations of geometries and frequencies at different density functional theory (DFT) and Hartree–Fock/Møller–Plesset (HF/MP2) levels have been performed. Results have been assessed and evaluated against those obtained at the coupled cluster single-double (Triplet) (CCSD(T)) level of theory. The characteristics of the C–Br and O–Br bonds have been identified via analysis of the electrostatic potential, natural bond orbital (NBO), and quantum theory of atoms in molecules (QTAIM). Analysis of the electrostatic potential (ESP) maps enabled the quantitative characterization of the Br σ-holes. Its magnitude seems very sensitive to the environment and the charge accumulated in the adjacent centers. Some quantum topological parameters, namely Ñ²ρ, ellipticity at bond critical points and the Laplacian bond order, were computed and discussed. The potential energy function for internal rotation has been computed and Fourier transformed to characterize the conformational preferences and origin of the barriers. NBO energetic components for rotation about the C–Br and O–Br bonds as a function of torsion angle have been computed and displayed. Full article

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Open AccessArticle

Exploring the Nature of Silicon-Noble Gas Bonds in H₃SiNgNSi and HSiNgNSi Compounds (Ng = Xe, Rn)

by Sudip Pan, Ranajit Saha and Pratim K. Chattaraj

Int. J. Mol. Sci. 2015, 16(3), 6402-6418; https://doi.org/10.3390/ijms16036402 - 19 Mar 2015

Cited by 38 | Viewed by 7500

Abstract

Ab initio and density functional theory-based computations are performed to investigate the structure and stability of H₃SiNgNSi and HSiNgNSi compounds (Ng = Xe, Rn). They are thermochemically unstable with respect to the dissociation channel producing Ng and H₃SiNSi or [...] Read more.

Ab initio and density functional theory-based computations are performed to investigate the structure and stability of H₃SiNgNSi and HSiNgNSi compounds (Ng = Xe, Rn). They are thermochemically unstable with respect to the dissociation channel producing Ng and H₃SiNSi or HSiNSi. However, they are kinetically stable with respect to this dissociation channel having activation free energy barriers of 19.3 and 23.3 kcal/mol for H₃SiXeNSi and H₃SiRnNSi, respectively, and 9.2 and 12.8 kcal/mol for HSiXeNSi and HSiRnNSi, respectively. The rest of the possible dissociation channels are endergonic in nature at room temperature for Rn analogues. However, one three-body dissociation channel for H₃SiXeNSi and one two-body and one three-body dissociation channels for HSiXeNSi are slightly exergonic in nature at room temperature. They become endergonic at slightly lower temperature. The nature of bonding between Ng and Si/N is analyzed by natural bond order, electron density and energy decomposition analyses. Natural population analysis indicates that they could be best represented as (H₃SiNg)⁺(NSi)⁻ and (HSiNg)⁺(NSi)⁻. Energy decomposition analysis further reveals that the contribution from the orbital term (ΔE_orb) is dominant (ca. 67%–75%) towards the total attraction energy associated with the Si-Ng bond, whereas the electrostatic term (ΔE_elstat) contributes the maximum (ca. 66%–68%) for the same in the Ng–N bond, implying the covalent nature of the former bond and the ionic nature of the latter. Full article

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Open AccessArticle

Multiscale Experimental and Theoretical Investigations of Spin Crossover Fe^II Complexes: Examples of [Fe(phen)₂(NCS)₂] and [Fe(PM-BiA)₂(NCS)₂]

by Samir F. Matar, Philippe Guionneau and Guillaume Chastanet

Int. J. Mol. Sci. 2015, 16(2), 4007-4027; https://doi.org/10.3390/ijms16024007 - 12 Feb 2015

Cited by 16 | Viewed by 7954

Abstract

For spin crossover (SCO) complexes, computation results are reported and confirmed with experiments at multiscale levels of the isolated molecule and extended solid on the one hand and theory on the other hand. The SCO phenomenon which characterizes organometallics based on divalent iron [...] Read more.

For spin crossover (SCO) complexes, computation results are reported and confirmed with experiments at multiscale levels of the isolated molecule and extended solid on the one hand and theory on the other hand. The SCO phenomenon which characterizes organometallics based on divalent iron in an octahedral FeN₆-like environment with high spin (HS) and low spin (LS) states involves the LS/HS switching at the cost of small energies provided by temperature, pressure or light, the latter connected with Light-Induced Excited Spin-State Trapping (LIESST) process. Characteristic infra red (IR) and Raman vibration frequencies are computed within density functional theory (DFT) framework. In [Fe(phen)₂(NCS)₂] a connection of selected frequencies is established with an ultra-fast light-induced LS → HS photoswitching mechanism. In the extended solid, density of state DOS and electron localization function (ELF) are established for both LS and HS forms, leading to characterizion of the compound as an insulator in both spin states with larger gaps for LS configuration, while keeping molecular features in the solid. In [Fe(PM-BiA)₂(NCS)₂], by combining DFT and classical molecular dynamics, the properties and the domains of existence of the different phases are obtained by expressing the potential energy surfaces in a short range potential for Fe–N interactions. Applying such Fe–N potentials inserted in a classical force field and carrying out molecular dynamics (MD) in so-called “semi-classical MD” calculations, lead to the relative energies of HS/LS configurations of the crystal and to the assessment of the experimental (P, T) phase diagram. Full article

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Open AccessArticle

Experimental and Theoretical Study of O-Substituent Effect on the Fluorescence of 8-Hydroxyquinoline

by Mohie E. M. Zayed, Reda M. El-Shishtawy, Shaaban A. Elroby, Abdullah Y. Obaid and Zahra M. Al-amshany

Int. J. Mol. Sci. 2015, 16(2), 3804-3819; https://doi.org/10.3390/ijms16023804 - 10 Feb 2015

Cited by 5 | Viewed by 10785

Abstract

The synthesis and characterization of different ether and ester derivatives of 8-hydroxyquinoline have been made. UV-visible and fluorescence spectra of these compounds have revealed spectral dependence on both solvent and O-substituent. The fluorescence intensity of ether derivatives revealed higher intensity for 8-octyloxyquinoline compared [...] Read more.

The synthesis and characterization of different ether and ester derivatives of 8-hydroxyquinoline have been made. UV-visible and fluorescence spectra of these compounds have revealed spectral dependence on both solvent and O-substituent. The fluorescence intensity of ether derivatives revealed higher intensity for 8-octyloxyquinoline compared with 8-methoxyquinoline, whereas those of ester derivatives had less fluorescence than 8-hydroxyquinoline. Theoretical calculations based on Time-dependent density functional theory (TD-DFT) were carried out for the quinolin-8-yl benzoate (8-OateQ) compound to understand the effect of O-substituent on the electronic absorption of 8-hydroxyquinaline (8-HQ). The calculations revealed comparable results with those obtained from the experimental data. Optimized geometrical structure was calculated with DFT at B3LYP/6-311++G** level of theory. The results indicated that 8-OateQ is not a coplanar structure. The absorption spectra of the compound were computed in gas-phase and solvent using B3LYP and CAM-B3LYP methods with 6-311++G ** basis set. The agreement between calculated and experimental wavelengths was very good at CAM-B3LYP/6-311++G** level of theory. Full article

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Open AccessArticle

Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

by Ohgi Takahashi, Ryota Kirikoshi and Noriyoshi Manabe

Int. J. Mol. Sci. 2015, 16(1), 1613-1626; https://doi.org/10.3390/ijms16011613 - 12 Jan 2015

Cited by 17 | Viewed by 9561

Abstract

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which [...] Read more.

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism. Full article

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Open AccessArticle

Excited States and Photodebromination of Selected Polybrominated Diphenyl Ethers: Computational and Quantitative Structure—Property Relationship Studies

by Jin Luo, Jiwei Hu, Xionghui Wei, Lingyun Li and Xianfei Huang

Int. J. Mol. Sci. 2015, 16(1), 1160-1178; https://doi.org/10.3390/ijms16011160 - 6 Jan 2015

Cited by 11 | Viewed by 7051

Abstract

This paper presents a density functional theory (DFT)/time-dependent DFT (TD-DFT) study on the lowest lying singlet and triplet excited states of 20 selected polybrominateddiphenyl ether (PBDE) congeners, with the solvation effect included in the calculations using the polarized continuum model (PCM). The results [...] Read more.

This paper presents a density functional theory (DFT)/time-dependent DFT (TD-DFT) study on the lowest lying singlet and triplet excited states of 20 selected polybrominateddiphenyl ether (PBDE) congeners, with the solvation effect included in the calculations using the polarized continuum model (PCM). The results obtained showed that for most of the brominated diphenyl ether (BDE) congeners, the lowest singlet excited state was initiated by the electron transfer from HOMO to LUMO, involving a π–σ* excitation. In triplet excited states, structure of the BDE congeners differed notably from that of the BDE ground states with one of the specific C–Br bonds bending off the aromatic plane. In addition, the partial least squares regression (PLSR), principal component analysis-multiple linear regression analysis (PCA-MLR), and back propagation artificial neural network (BP-ANN) approaches were employed for a quantitative structure-property relationship (QSPR) study. Based on the previously reported kinetic data for the debromination by ultraviolet (UV) and sunlight, obtained QSPR models exhibited a reasonable evaluation of the photodebromination reactivity even when the BDE congeners had same degree of bromination, albeit different patterns of bromination. Full article

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Open AccessArticle

Structure–Biological Function Relationship Extended to Mitotic Arrest-Deficient 2-Like Protein Mad2 Native and Mutants-New Opportunity for Genetic Disorder Control

by Speranta Avram, Adina Milac, Maria Mernea, Dan Mihailescu, Mihai V. Putz and Catalin Buiu

Int. J. Mol. Sci. 2014, 15(11), 21381-21400; https://doi.org/10.3390/ijms151121381 - 18 Nov 2014

Cited by 4 | Viewed by 6012

Abstract

Overexpression of mitotic arrest-deficient proteins Mad1 and Mad2, two components of spindle assembly checkpoint, is a risk factor for chromosomal instability (CIN) and a trigger of many genetic disorders. Mad2 transition from inactive open (O-Mad2) to active closed (C-Mad2) conformations or Mad2 binding [...] Read more.

Overexpression of mitotic arrest-deficient proteins Mad1 and Mad2, two components of spindle assembly checkpoint, is a risk factor for chromosomal instability (CIN) and a trigger of many genetic disorders. Mad2 transition from inactive open (O-Mad2) to active closed (C-Mad2) conformations or Mad2 binding to specific partners (cell-division cycle protein 20 (Cdc20) or Mad1) were targets of previous pharmacogenomics studies. Here, Mad2 binding to Cdc20 and the interconversion rate from open to closed Mad2 were predicted and the molecular features with a critical contribution to these processes were determined by extending the quantitative structure-activity relationship (QSAR) method to large-size proteins such as Mad2. QSAR models were built based on available published data on 23 Mad2 mutants inducing CIN-related functional changes. The most relevant descriptors identified for predicting Mad2 native and mutants action mechanism and their involvement in genetic disorders are the steric (van der Waals area and solvent accessible area and their subdivided) and energetic van der Waals energy descriptors. The reliability of our QSAR models is indicated by significant values of statistical coefficients: Cross-validated correlation q² (0.53–0.65) and fitted correlation r² (0.82–0.90). Moreover, based on established QSAR equations, we rationally design and analyze nine de novo Mad2 mutants as possible promoters of CIN. Full article

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527 KiB

Open AccessArticle

3D QSAR Studies, Pharmacophore Modeling and Virtual Screening on a Series of Steroidal Aromatase Inhibitors

by Huiding Xie, Kaixiong Qiu and Xiaoguang Xie

Int. J. Mol. Sci. 2014, 15(11), 20927-20947; https://doi.org/10.3390/ijms151120927 - 14 Nov 2014

Cited by 23 | Viewed by 6899 | Correction

Abstract

Aromatase inhibitors are the most important targets in treatment of estrogen-dependent cancers. In order to search for potent steroidal aromatase inhibitors (SAIs) with lower side effects and overcome cellular resistance, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were [...] Read more.

Aromatase inhibitors are the most important targets in treatment of estrogen-dependent cancers. In order to search for potent steroidal aromatase inhibitors (SAIs) with lower side effects and overcome cellular resistance, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of SAIs to build 3D QSAR models. The reliable and predictive CoMFA and CoMSIA models were obtained with statistical results (CoMFA: q² = 0.636, r²_ncv = 0.988, r²_pred = 0.658; CoMSIA: q² = 0.843, r²_ncv = 0.989, r²_pred = 0.601). This 3D QSAR approach provides significant insights that can be used to develop novel and potent SAIs. In addition, Genetic algorithm with linear assignment of hypermolecular alignment of database (GALAHAD) was used to derive 3D pharmacophore models. The selected pharmacophore model contains two acceptor atoms and four hydrophobic centers, which was used as a 3D query for virtual screening against NCI2000 database. Six hit compounds were obtained and their biological activities were further predicted by the CoMFA and CoMSIA models, which are expected to design potent and novel SAIs. Full article

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992 KiB

Open AccessReview

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

by Peter I. Nagy

Int. J. Mol. Sci. 2014, 15(11), 19562-19633; https://doi.org/10.3390/ijms151119562 - 28 Oct 2014

Cited by 144 | Viewed by 16481

Abstract

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the [...] Read more.

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. Full article

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761 KiB

Open AccessReview

Influence of Sulfur for Oxygen Substitution in the Solvolytic Reactions of Chloroformate Esters and Related Compounds

by Malcolm J. D'Souza and Dennis N. Kevill

Int. J. Mol. Sci. 2014, 15(10), 18310-18332; https://doi.org/10.3390/ijms151018310 - 10 Oct 2014

Cited by 7 | Viewed by 8748

Abstract

The replacement of oxygen within a chloroformate ester (ROCOCl) by sulfur can lead to a chlorothioformate (RSCOCl), a chlorothionoformate (ROCSCl), or a chlorodithioformate (RSCSCl). Phenyl chloroformate (PhOCOCl) reacts over the full range of solvents usually included in Grunwald-Winstein equation studies of solvolysis by [...] Read more.

The replacement of oxygen within a chloroformate ester (ROCOCl) by sulfur can lead to a chlorothioformate (RSCOCl), a chlorothionoformate (ROCSCl), or a chlorodithioformate (RSCSCl). Phenyl chloroformate (PhOCOCl) reacts over the full range of solvents usually included in Grunwald-Winstein equation studies of solvolysis by an addition-elimination (A-E) pathway. At the other extreme, phenyl chlorodithioformate (PhSCSCl) reacts across the range by an ionization pathway. The phenyl chlorothioformate (PhSCOCl) and phenyl chlorothionoformate (PhOCSCl) react at remarkably similar rates in a given solvent and there is a dichotomy of behavior with the A-E pathway favored in solvents such as ethanol-water and the ionization mechanism favored in aqueous solvents rich in fluoroalcohol. Alkyl esters behave similarly but with increased tendency to ionization as the alkyl group goes from 1° to 2° to 3°. N,N-Disubstituted carbamoyl halides favor the ionization pathway as do also the considerably faster reacting thiocarbamoyl chlorides. The tendency towards ionization increases as, within the three contributing structures of the resonance hybrid for the formed cation, the atoms carrying positive charge (other than the central carbon) change from oxygen to sulfur to nitrogen, consistent with the relative stabilities of species with positive charge on these atoms. Full article

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905 KiB

Open AccessArticle

Deactivation of 6-Aminocoumarin Intramolecular Charge Transfer Excited State through Hydrogen Bonding

by Ewa Krystkowiak, Krzysztof Dobek and Andrzej Maciejewski

Int. J. Mol. Sci. 2014, 15(9), 16628-16648; https://doi.org/10.3390/ijms150916628 - 19 Sep 2014

Cited by 10 | Viewed by 7226

Abstract

This paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in various aprotic hydrogen-bond forming solvents. It was established that solvent polarity as well as hydrogen-bonding ability influence solute properties. The hydrogen-bonding interactions between S₁-electronic [...] Read more.

This paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in various aprotic hydrogen-bond forming solvents. It was established that solvent polarity as well as hydrogen-bonding ability influence solute properties. The hydrogen-bonding interactions between S₁-electronic excited solute and solvent molecules were found to facilitate the nonradiative deactivation processes. The energy-gap dependence on radiationless deactivation in aprotic solvents was found to be similar to that in protic solvents. Full article

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2009

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5091 KiB

Open AccessReview

Chemical Interactions and Their Role in the Microphase Separation of Block Copolymer Thin Films

by Richard A. Farrell, Thomas G. Fitzgerald, Dipu Borah, Justin D. Holmes and Michael A. Morris

Int. J. Mol. Sci. 2009, 10(9), 3671-3712; https://doi.org/10.3390/ijms10093671 - 25 Aug 2009

Cited by 91 | Viewed by 18998

Abstract

The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are [...] Read more.

The thermodynamics of self-assembling systems are discussed in terms of the chemical interactions and the intermolecular forces between species. It is clear that there are both theoretical and practical limitations on the dimensions and the structural regularity of these systems. These considerations are made with reference to the microphase separation that occurs in block copolymer (BCP) systems. BCP systems self-assemble via a thermodynamic driven process where chemical dis-affinity between the blocks driving them part is balanced by a restorative force deriving from the chemical bond between the blocks. These systems are attracting much interest because of their possible role in nanoelectronic fabrication. This form of self-assembly can obtain highly regular nanopatterns in certain circumstances where the orientation and alignment of chemically distinct blocks can be guided through molecular interactions between the polymer and the surrounding interfaces. However, for this to be possible, great care must be taken to properly engineer the interactions between the surfaces and the polymer blocks. The optimum methods of structure directing are chemical pre-patterning (defining regions on the substrate of different chemistry) and graphoepitaxy (topographical alignment) but both centre on generating alignment through favourable chemical interactions. As in all self-assembling systems, the problems of defect formation must be considered and the origin of defects in these systems is explored. It is argued that in these nanostructures equilibrium defects are relatively few and largely originate from kinetic effects arising during film growth. Many defects also arise from the confinement of the systems when they are ‘directed’ by topography. The potential applications of these materials in electronics are discussed. Full article

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309 KiB

Open AccessCommunication

Anomalously Strong Effect of the Ion Sign on the Thermochemistry of Hydrogen Bonded Aqueous Clusters of Identical Chemical Composition

by Alexey B. Nadykto, Fangqun Yu and Anas Al Natsheh

Int. J. Mol. Sci. 2009, 10(2), 507-517; https://doi.org/10.3390/ijms10020507 - 5 Feb 2009

Cited by 8 | Viewed by 13768

Abstract

The sign preference of hydrogen bonded aqueous ionic clusters Χ±(H₂O)_i (n =1-5, Χ = F; Cl; Br) has been investigated using the Density Functional Theory and ab initio MP2 method. The present study indicates the anomalously large [...] Read more.

The sign preference of hydrogen bonded aqueous ionic clusters Χ±(H₂O)_i (n =1-5, Χ = F; Cl; Br) has been investigated using the Density Functional Theory and ab initio MP2 method. The present study indicates the anomalously large difference in formation free energies between cations and anions of identical chemical composition. The effect of vibrational anharmonicity on stepwise Gibbs free energy changes has been investigated, and possible uncertainties associated with the harmonic treatment of vibrational spectra have been discussed. Full article

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2008

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408 KiB

Open AccessCommunication

Effect of Ammonia on the Gas-Phase Hydration of the Common Atmospheric Ion HSO₄^-

by Alexey B. Nadykto, Fangqun Yu and Jason Herb

Int. J. Mol. Sci. 2008, 9(11), 2184-2193; https://doi.org/10.3390/ijms9112184 - 7 Nov 2008

Cited by 24 | Viewed by 17335

Abstract

Hydration directly affects the mobility, thermodynamic properties, lifetime and nucleation rates of atmospheric ions. In the present study, the role of ammonia on the formation of hydrogen bonded complexes of the common atmospheric hydrogensulfate (HSO₄^-) ion with water has been [...] Read more.

Hydration directly affects the mobility, thermodynamic properties, lifetime and nucleation rates of atmospheric ions. In the present study, the role of ammonia on the formation of hydrogen bonded complexes of the common atmospheric hydrogensulfate (HSO₄^-) ion with water has been investigated using the Density Functional Theory (DFT). Our findings rule out the stabilizing effect of ammonia on the formation of negatively charged cluster hydrates and show clearly that the conventional (classical) treatment of ionic clusters as presumably more stable compared to neutrals may not be applicable to pre-nucleation clusters. These considerations lead us to conclude that not only quantitative but also qualitative assessment of the relative thermodynamic stability of atmospheric clusters requires a quantum-chemical treatment. Full article

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695 KiB

Open AccessArticle

Li_x@C₆₀: Calculations of the Encapsulation Energetics and Thermodynamics

by Zdeněk Slanina, Filip Uhlík, Shyi-Long Lee, Ludwik Adamowicz and Shigeru Nagase

Int. J. Mol. Sci. 2008, 9(9), 1841-1850; https://doi.org/10.3390/ijms9091841 - 17 Sep 2008

Cited by 13 | Viewed by 11275

Abstract

Li@C₆₀ and Li@C₇₀ can be prepared and thus, their calculations at higher levels of theory are also of interest. In the report, the computations are carried out on Li@C60, Li₂@C₆₀ and Li₃@C₆₀ with the B3LYP [...] Read more.

Li@C₆₀ and Li@C₇₀ can be prepared and thus, their calculations at higher levels of theory are also of interest. In the report, the computations are carried out on Li@C60, Li₂@C₆₀ and Li₃@C₆₀ with the B3LYP density-functional theory treatment in the standard 3-21G and 6-31G* basis sets. The computed energetics suggests that Li_x@C₆₀ species may be produced for a few small x values if the Li pressure is enhanced sufficiently. In order to check the suggestion, a deeper computational evaluation of the encapsulation thermodynamics is carried out. Full article

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319 KiB

Open AccessArticle

Exact and Effective Pair-Wise Potential for Protein-Ligand Interactions Obtained from a Semiempirical Energy Partition

by Alexandre R. F. Carvalho, André T. Puga and André Melo

Int. J. Mol. Sci. 2008, 9(9), 1652-1664; https://doi.org/10.3390/ijms9091652 - 2 Sep 2008

Cited by 1 | Viewed by 11450

Abstract

In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I) and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT) terms, was introduced [...] Read more.

In this work, the partition method introduced by Carvalho and Melo was used to study the complex between Cucurbita maxima trypsin inhibitor (CMTI-I) and glycerol at the AM1 level. An effective potential, combining non-bonding and polarization plus charge transfer (PLCT) terms, was introduced to evaluate the magnitude of the interaction between each amino acid and the ligand. In this case study, the nonbonding–PLCT noncompensation characterizes the stabilization energy of the association process in study. The main residues (Gly29, Cys3 and Arg5) with net attractive effects and Arg1 (with a net repulsive effect), responsible by the stability of protein-ligand complex, are associated with large nonbonding energies non-compensated by PLCT effects. The results obtained enable us to conclude that the present decomposition scheme can be used for understanding the cohesive phenomena in proteins. Full article

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728 KiB

Open AccessReview

Density Functionals of Chemical Bonding

by Mihai V. Putz

Int. J. Mol. Sci. 2008, 9(6), 1050-1095; https://doi.org/10.3390/ijms9061050 - 26 Jun 2008

Cited by 48 | Viewed by 15504

Abstract

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps [...] Read more.

The behavior of electrons in general many-electronic systems throughout the density functionals of energy is reviewed. The basic physico-chemical concepts of density functional theory are employed to highlight the energy role in chemical structure while its extended influence in electronic localization function helps in chemical bonding understanding. In this context the energy functionals accompanied by electronic localization functions may provide a comprehensive description of the global-local levels electronic structures in general and of chemical bonds in special. Becke-Edgecombe and author’s Markovian electronic localization functions are discussed at atomic, molecular and solid state levels. Then, the analytical survey of the main workable kinetic, exchange, and correlation density functionals within local and gradient density approximations is undertaken. The hierarchy of various energy functionals is formulated by employing both the parabolic and statistical correlation degree of them with the electronegativity and chemical hardness indices by means of quantitative structure-property relationship (QSPR) analysis for basic atomic and molecular systems. Full article

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481 KiB

Open AccessArticle

Bonding in Mercury-Alkali Molecules: Orbital-driven van der Waals Complexes

by Elfi Kraka and Dieter Cremer

Int. J. Mol. Sci. 2008, 9(6), 926-942; https://doi.org/10.3390/ijms9060926 - 2 Jun 2008

Cited by 7 | Viewed by 10683

Abstract

The bonding situation in mercury-alkali diatomics HgA (²Σ⁺) (A = Li, Na, K, Rb) has been investigated employing the relativistic all-electron method Normalized Elimination of the Small Component (NESC), CCSD(T), and augmented VTZ basis sets. Although Hg,A interactions are [...] Read more.

The bonding situation in mercury-alkali diatomics HgA (²Σ⁺) (A = Li, Na, K, Rb) has been investigated employing the relativistic all-electron method Normalized Elimination of the Small Component (NESC), CCSD(T), and augmented VTZ basis sets. Although Hg,A interactions are typical of van der Waals complexes, trends in calculated De values can be explained on the basis of a 3-electron 2-orbital model utilizing calculated ionization potentials and the De values of HgA⁺(¹Σ⁺) diatomics. HgA molecules are identified as orbital-driven van der Waals complexes. The relevance of results for the understanding of the properties of liquid alkali metal amalgams is discussed. Full article

904 KiB

Open AccessArticle

Closing in on Chemical Bonds by Opening up Relativity Theory

by Cynthia Kolb Whitney

Int. J. Mol. Sci. 2008, 9(3), 272-298; https://doi.org/10.3390/ijms9030272 - 12 Mar 2008

Cited by 7 | Viewed by 9994

Abstract

This paper develops a connection between the phenomenology of chemical bonding and the theory of relativity. Empirical correlations between electron numbers in atoms and chemical bond stabilities in molecules are first reviewed and extended. Quantitative chemical bond strengths are then related to ionization [...] Read more.

This paper develops a connection between the phenomenology of chemical bonding and the theory of relativity. Empirical correlations between electron numbers in atoms and chemical bond stabilities in molecules are first reviewed and extended. Quantitative chemical bond strengths are then related to ionization potentials in elements. Striking patterns in ionization potentials are revealed when the data are viewed in an element-independent way, where element-specific details are removed via an appropriate scaling law. The scale factor involved is not explained by quantum mechanics; it is revealed only when one goes back further, to the development of Einstein’s special relativity theory. Full article

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2007

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372 KiB

Open AccessArticle

Chromatographic Retention Times of Polychlorinated Biphenyls: from Structural Information to Property Characterization

by Lorentz Jäntschi, Sorana D. Bolboaca and Mircea V. Diudea

Int. J. Mol. Sci. 2007, 8(11), 1125-1157; https://doi.org/10.3390/i8111125 - 22 Nov 2007

Cited by 20 | Viewed by 9524

Abstract

The paper presents a unitary approach of the use of a Molecular DescriptorsFamily in structure-property/activity relationships, particularly in modelling thechromatographic retention times of polychlorinated biphenyls. Starting from molecularstructure, viewed as a graph, and considering the bonds and bond types, atom types andoften the [...] Read more.

The paper presents a unitary approach of the use of a Molecular DescriptorsFamily in structure-property/activity relationships, particularly in modelling thechromatographic retention times of polychlorinated biphenyls. Starting from molecularstructure, viewed as a graph, and considering the bonds and bond types, atom types andoften the 3D geometry of the molecule, a huge family of molecular descriptors called MDFwas calculated. A preliminary selection of MDF members was done by simple linearregression (LR) against the measured property. The best fitted MDF subset is thensubmitted to multivariate linear regression (MLR) analysis in order to find the best pairs ofMDF members that produce a reliable QSPR (Quantitative Structure-PropertyRelationship) model. The predictive capability was finally tested by randomly splitting ofdata into training and test sets. The best obtained models are presented and the results arediscussed. Full article

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874 KiB

Open AccessArticle

Three Dimensional Pharmacophore Modelling of Monoamine oxidase-A (MAO-A) inhibitors

by Kalapatapu V.V.M. Sairam, Roop K. Khar, Rama Mukherjee and Swatantra K. Jain

Int. J. Mol. Sci. 2007, 8(9), 894-919; https://doi.org/10.3390/i8090894 - 3 Sep 2007

Cited by 5 | Viewed by 10252

Abstract

Flavoprotein monoamine oxidase is located on the outer membrane ofmitochondria. It catalyzes oxidative deamination of monoamine neurotransmitters such asserotonin, norepinephrine and dopamine and hence is a target enzyme for antidepressantdrugs. MAO (mono amine oxidase) has two isoforms, namely MAO-A and MAO-B.MAO-A isoform has [...] Read more.

Flavoprotein monoamine oxidase is located on the outer membrane ofmitochondria. It catalyzes oxidative deamination of monoamine neurotransmitters such asserotonin, norepinephrine and dopamine and hence is a target enzyme for antidepressantdrugs. MAO (mono amine oxidase) has two isoforms, namely MAO-A and MAO-B.MAO-A isoform has higher affinity for serotonin and norepinephrine, while; MAO-Bpreferentially deaminates phenylethylamine and benzylamine. These important propertiesdetermine the clinical importance of MAO inhibitors. Selective MAO-A inhibitors are usedin the treatment of neurological disorders such as depression. In this article we havedeveloped a Hypogen pharmacophore for a set of 64 coumarin analogs and tried to analyzethe intermolecular H-bonds with receptor structure. Full article

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