Molecular Electron Density Distribution Research Articles

DFT, Molecular Docking, Bioactivity and ADME Analyses of Vic-dioxim Ligand Containing Hydrazone Group and its Zn(II) Complex.

Cancer is one of the diseases affecting a large population worldwide and resulting in death. Finding new anti-cancer drugs that are target-focused and have low toxicity is of great importance. This study aimed to investigate the effects of vic-dioxime derivatives carrying hydrazone group and its Zn(II) complex on cancer using molecular docking, bioactivity and quantum chemical calculations. Molecular docking studies were performed on epidermal growth factor receptor and vascular endothelial growth factor receptor 2 target proteins. Furthermore, molecular geometry was performed, and the frontier molecular orbitals, Mulliken charges and molecular electron density distribution were evaluated using density functional theory. Also, the bioactivity parameters of the compounds were evaluated, and ADME analysis was performed using web-based tools. Higher binding affinity was observed for Zn(II) complex with target proteins vascular endothelial growth factor receptor 2 and against epidermal growth factor receptor when compared with LH2. Only the Zn(II) complex against the epidermal growth factor receptor had ligand efficiency and fit quality in the valid range. Furthermore, LH2 has the most potent electrophilic ability (acceptor) among other compounds. Moreover, both LH2 and Zn(II) complexes strongly satisfy Lipinski's rule of five. In conclusion, these novel compounds, especially Zn(II) complex, can be new candidates for anticancer drug development studies which are target-focused and have low toxicity.

Direct Observation of Polaritonic Chemistry by Nuclear Magnetic Resonance Spectroscopy

AbstractPolaritonic chemistry is emerging as a powerful approach to modifying the properties and reactivity of molecules and materials. However, probing how the electronics and dynamics of molecular systems change under strong coupling has been challenging due to the narrow range of spectroscopic techniques that can be applied in situ. Here we develop microfluidic optical cavities for vibrational strong coupling (VSC) that are compatible with nuclear magnetic resonance (NMR) spectroscopy using standard liquid NMR tubes. VSC is shown to influence the equilibrium between two conformations of a molecular balance sensitive to London dispersion forces, revealing an apparent change in the equilibrium constant under VSC. In all compounds studied, VSC does not induce detectable changes in chemical shifts, J‐couplings, or spin‐lattice relaxation times. This unexpected finding indicates that VSC does not substantially affect molecular electron density distributions, and in turn has profound implications for the possible mechanisms at play in polaritonic chemistry under VSC and suggests that the emergence of collective behavior is critical.

Direct Observation of Polaritonic Chemistry by Nuclear Magnetic Resonance Spectroscopy.

Polaritonic chemistry is emerging as a powerful approach to modifying the properties and reactivity of molecules and materials. However, probing how the electronics and dynamics of molecular systems change under strong coupling has been challenging due to the narrow range of spectroscopic techniques that can be applied in situ. Here we develop microfluidic optical cavities for vibrational strong coupling (VSC) that are compatible with nuclear magnetic resonance (NMR) spectroscopy using standard liquid NMR tubes. VSC is shown to influence the equilibrium between two conformations of a molecular balance sensitive to London dispersion forces, revealing an apparent change in the equilibrium constant under VSC. In all compounds studied, VSC does not induce detectable changes in chemical shifts, J-couplings, or spin-lattice relaxation times. This unexpected finding indicates that VSC does not substantially affect molecular electron density distributions, and in turn has profound implications for the possible mechanisms at play in polaritonic chemistry under VSC and suggests that the emergence of collective behavior is critical.

Alkali and Transition Metal-Doped 15-Crown-5 with Enhanced Nonlinear Optical Response: A DFT Study

In this study, geometries, electronic structure and first hyperpolarizability of metals doped 15-crown-5 (C5M) were explored through the density functional theory (DFT) method. Alkali metals (Li, Na, K) and silver (Ag) were placed inside and outside of the crown ether, respectively, to deliver three compounds designated as Li[C5M]Ag, Na[C5M]Ag and K[C5M]Ag. All designed complexes were optimized at singlet, triplet, quintet and septet states, where the singlet state was identified as the stable state. The influence of doping on C5M can be investigated by energy gap fluctuation and it was noted that the smallest energy gap (4.68[Formula: see text]eV) was exhibited by K[C5M]Ag among all the intentional complexes, in contrast to reference C5M (12.73[Formula: see text]eV). Moreover, the density of state (DOS), transition density matrix (TDM), noncovalent interaction (NCI), molecular electrostatic potential (MESP) and electron density distribution map (EDDM) analysis were implemented. Static isotropic polarizability values were observed in the range of [Formula: see text]–[Formula: see text] esu which were comparable to dynamic isotropic polarizability values; [Formula: see text]–[Formula: see text]. Li[C5M]Ag revealed maximum first hyperpolarizability ([Formula: see text]) of [Formula: see text][Formula: see text]esu with the minimum transition energy ([Formula: see text]) of 2.93[Formula: see text]eV.

A Proposed Insight into the Anti-viral Potential of Silver Nanoparticles against Novel Coronavirus Disease (COVID-19)

This article presents a proposed insight into the anti-viral potential of silver nanoparticles against novel coronavirus disease (COVID-19). Possible mechanisms of influence of silver nanoparticles on the coronavirus are considered. Models of nanosilver complexes with spike protein of coronavirus amino acids were constructed using computer quantum-chemical modeling. The values of electron density distribution, highest occupied molecular orbital, lowest unoccupied molecular orbital and electron density distribution gradient for each constructed model are obtained. Analysis of the obtained data showed that the most energy-efficient interaction is the formation of the "tryptophan–nanosilver" complex (E= - 5856.83 kkal/mol). According to the results of quantum chemical calculations, the most stable complex is the "cysteine– Ag nanoparticles" complex (ΔE = 0.16 a. u.).

Pnictogen effects on the electronic interactions in the Lewis pair complexes Ph3EB(C6F5)3 (E = P, As, Sb)

Lewis pair complexes bearing a BR3 acid and a R’3E base (E = P, As, Sb; R, R’ – organic ligands) play key roles in modern chemistry and technology, their properties being strongly relevant to catalysis and material science. The donor acceptor complexes Ph3EB(C6F5)3 attract special interest due to the elongated E-B bond that shifts the molecular parameters towards those of a frustrated Lewis pair. In depth theoretical and experimental studies of the Ph3EB(C6F5)3 systems presented in this work provide new insights into the nature of intramolecular electronic interactions in these molecules. A missing X-ray structure of Ph3AsB(C6F5)3 is described. Analyses of molecular structures, orbitals, dissociation energies and electron density distributions reveal crucial influence of non-covalent interactions on the Ph3EB(C6F5)3 stability.

Probing Bias-Induced Electron Density Shifts in Metal-Molecule Interfaces via Tip-Enhanced Raman Scattering.

Surface charging effects at metal-molecule interfaces, for example, charge transfer, charge transport, charge injection, and so on, have a strong impact on the performance of organic electronics. Only having molecules bound or adsorbed on different metals results in a doping-like behavior at the interface by the different work functions of the metals and creates hybrid surface states, which strongly affect the efficiencies. With the ongoing downsizing and thinning of the organic components, the impact of the interface will even further increase. However, most of the investigations only monitor the interface without the additional charging effects from applying a voltage to the interface. In this work we present a spectroscopic approach based on tip-enhanced Raman spectroscopy (TERS) to study metal-molecule interfaces with an applied voltage simulating the electric field strength in real devices. We monitor how an intrinsic inductive effect of partial functional groups in molecules can shift the molecular electron density (ED) distribution when a bias voltage is applied. Therefore, we choose two molecules as model systems, which are similar in size and binding condition to a smooth gold surface, but with different electronic structure. By placing the tip 1 nm over the molecular surface at a fixed position and changing the applied bias voltage, we record electric-field-dependent tip-enhanced Raman spectra. Specific vibrational bands exhibit voltage-dependent intensity changes related to the shift of the local ED inside the molecules. We believe this experiment is valuable to gain deeper insights into charged metal-molecule interfaces.

Theoretical Prediction on the New Types of Noble Gas Containing Anions OBONgO- and OCNNgO- (Ng = He, Ar, Kr and Xe).

The fluorine-less noble gas containing anions OBONgO− and OCNNgO− have been studied by correlated electronic structure calculation and density functional theory. The obtained energetics indicates that for Ng=Kr and Xe, these anions should be kinetically stable at low temperature. The molecular structures and electron density distribution suggests that these anions are stabilized by ion-induced dipole interactions with charges concentrated on the electronegative OBO and OCN groups. The current study shows that in addition to the fluoride ion, polyatomic groups with strong electronic affinities can also form stable noble gas containing anions of the type Y−…NgO.

Electron densities of two cyclononapeptides from invariom application

Abstract The nonapeptides cyclo(Val-Leu-Pro-Ile-Leu-Leu-Leu-Val-Leu) (I) and cyclo(Val-Leu-Pro-Ala-Leu-Leu-Leu-Val-Leu) (II) were identified as promising candidates for the development as potential anti-cancer drugs. We report a re-refinement of deposited single-crystal X-ray diffraction data with aspherical scattering factors from the invariom database. A subsequent evaluation of the molecular electron density distribution and of the differences in their molecular electrostatic potentials provides insight in their activities. The sequences differ only in residue 4, Ile in (I) and Ala in (II). Since the anti-tumor potency is reduced for the Ala peptide (II), the causes for the differences seen in activity between (I) and (II) were examined from a structural and from an electron density (ED) point of view. The exchange at residue 4 does not lead to significant changes in molecular geometry. Molecular Hirshfeld surfaces and electrostatic potential (ESP) isosurfaces show accumulations of intermolecular interactions in regions adjacent to the Ile/Ala residues indicating preferred interactions with a potential receptor in these regions. The concentrations of intermolecular interactions were localized on the Hirshfeld surfaces through an extended basin of ED concentration close to the Ile/Ala residues. Differences in the electrostatic potentials (ESPs) between (I) and (II) were only found at the Ile/Ala site and were very close to zero otherwise.

Molecular Electron Density Distribution and X-Ray Diffraction Patterns of Smectic A Liquid Crystals - A Simulation Study.

X-ray diffraction (XRD) is one of the most important methods to assess the long-range translational order in smectic A (SmA) liquid crystals. Nevertheless, the knowledge about the influence of the molecular electron density distribution (MEDD) on the XRD pattern is rather limited because it is not possible to vary the orientational order, the translational order and the MEDD independently in an experiment. We here present a systematic simulation study in which we examine this effect and show that the MEDD indeed has a major impact on the general appearance of the XRD pattern. More specifically, we find that the smectic layer peaks and the intensity ratios thereof strongly depend on the width of the MEDD. The classic approach by Leadbetter et al. to determine the smectic translational order parameter from XRD intensities works if the MEDD is quite narrow. In all other cases the influence of the MEDD has to be taken into account.

Two faces of triel bonds in boron trihalide complexes.

The N⋅⋅⋅B triel bonds in complexes of boron trihalides, BX3 (X = F, Cl, Br, and I), with species acting as Lewis bases through the nitrogen center, NH3 , N2 , and HCN, are analyzed theoretically (MP2/aug-cc-pVTZ calculations). It is confirmed that stronger Lewis acid properties of the boron center are observed for the BCl3 moiety than for the BF3 one in complexes with the strong Lewis base (NH3 ); while the opposite order is observed for complexes with the weak Lewis base (N2 ). The BX3 NCH complexes (for X = Cl, Br, and I) are characterized by two tautomeric forms and by two corresponding N⋅⋅⋅B distances, the shorter one possesses characteristics of the covalent bond. In a case of the BF3 NCH complex one energetic minimum is observed. Ab initio calculations are supported by an analysis of molecular electrostatic potentials (EPs) and electron density distributions. The quantum theory of 'atoms in molecules' and the decomposition of the energy of interaction are applied. The aforementioned acidity orders as well as the existence of two tautomers for some of complexes result partly from the electrostatic interactions' balance; the EP distribution is different for the BF3 species than for the other BX3 species where X = Cl, Br, and I. © 2017 Wiley Periodicals, Inc.

The role of halogen interactions in the crystal structure of biscyclopentadienyl dihalides

The purpose of this survey is to examine the crystal packing of bent metallocenes, namely, group IV, V and VI biscyclopentadienyl dihalides and dihydrides, first synthesized in the late 1950s. This analysis is based on the present knowledge on new types of intermolecular contacts such as halogen and C–H⋯π interactions as well as dihydrogen bonds. Results are also supported by ab initio calculations that provide information on electrostatic charge distributions, in particular the effect of two V-shaped metal–halogen bonds on the molecular electron density distribution. Type I halogen interactions do not appear to be affected by this feature, specifically the geometric parameters and variation of atom polarizability, but the resultant electronic density distribution precludes the presence of Type II halogen bonds. Special attention is given to the competition among hydrogen and halogen interactions, in particular its influence on the nature and geometric orientations of the different supramolecular motifs and, ultimately, on the space groups observed for each crystal.

Optical properties and component composition of layers of cyanine dyes on dielectric supports: influence of asymmetry of the molecular electron density distribution

The component composition of molecular layers of dicarbocyanine dyes of cationic type on glass is determined by the absorption spectroscopy methods. For symmetric and asymmetric molecules the component composition depends on the chemical structure of a molecule and its interaction with the substrate, which are responsible for the electron density distribution in a molecule. The interaction with the substrate depends on the thickness of a layer and the orientation of a layer molecule on the substrate. The increase in the separation between the molecule and the substrate in thicker layers decreases the interaction with the substrate and the asymmetry of a molecule. In symmetric and slightly asymmetric dyes the value of the charge difference on the end groups decreases with increasing layer thickness, whereas in dyes with a large asymmetry, both the value and the sign of the charge difference change. The above results are confirmed by data on the computer simulation of the charge distribution in a dicarbocyanine cation upon its interaction with the oxygen anion on the substrate.

Unification of molecular NIR fluorescence and aggregation-induced blue emission via novel dendritic zinc phthalocyanines

In this work, novel dendritic zinc phthalocyanines showing both molecular NIR fluorescence and aggregation-induced emission characteristics have been successfully synthesized via a two-step reaction on the basis of bisphthalonitrile precursors with different electron donor–conjugation–acceptor (D–π–A) structures. The luminescent properties of the resultant dendritic zinc phthalocyanines were fully investigated in N, N-dimethylformamide (DMF) solution, in DMF/H2O mixed solvent, in the solid state as well as polymethylmethacrylate composite film. The dendritic zinc phthalocyanines substituted with hydroquinone, naphthalenediol, or dihydroxybiphenyl moieties exhibited an unusual luminescence changes from highly near infrared (NIR) emitting in molecular state to strongly blue fluorescence in aggregated state as well as solid state, where the maximum fluorescent emission wavelength and highest quantum yield were detected from dendritic zinc phthalocyanines containing naphthalenediol and dihydroxybiphenyl groups, respectively. On the contrary, dendritic zinc phthalocyanines bearing diphenylmethane or bisphenol A units only exhibit NIR fluorescent emission in their molecular state. The distinct fluorescent emissions for these dendritic zinc phthalocyanines are rationalized in the framework of molecular configuration and electron density distribution as clarified by density functional theory (DFT) calculation. Moreover, the well-organized three-dimensional microspheres composed of abundant rod-like building blocks were discovered via the self-assembly of dendritic zinc phthalocyanine molecules in DMF/H2O (50/50 vol%) mixture.

Preparation of alginate-chitosan-cyclodextrin micro- and nanoparticles loaded with anti-tuberculosis compounds.

This paper describes the synthesis and application of alginate–chitosan–cyclodextrin micro- and nanoparticulate systems loaded with isoniazid (INH) and isoconazole nitrate (ISN) as antimycobacterial compounds. Preparation and morphology of the obtained particles, as well as antimycobacterial activity data of the obtained systems are presented. Docking of isoconazole into the active site of enoyl–acyl carrier protein reductase (InhA) of Mycobacetrium tuberculosis was carried out in order to predict the binding affinity and non-covalent interactions stabilizing the InhA–isoconazole complex. To assess these interactions, frontier molecular orbital calculations were performed for the active site of InhA and isoconazole obtained from docking. Isoconazole was predicted to be an active inhibitor of InhA with the analysis of the molecular docking and electron density distribution. It has been detected that alginate–chitosan–cyclodextrin microparticulate systems loaded with INH and ISN are as effective as pure INH applied in higher dosages.

Antioxidant potential of orientin: A combined experimental and DFT approach

The antioxidant activity of the bioactive fractions obtained from the leaves of Rhynchosia capitata is evaluated for its capacity to reduce ferric ions. In vitro antihemolytic analysis for the separated erythrocytes of Wistar rat blood cells exhibits maximum inhibition value for ethyl acetate (1202.55±9.46) than ethanol fraction (424.57±12.04). Gas and solvent phase studies of structural and molecular characteristics of C-glycosyl flavonoid, orientin present in the bioactive fraction of R. capitata is investigated through hydrogen atom transfer mechanism (HAT) using DFT/B3LYP/6-311G(d,p) level of theory. Interestingly, the intramolecular hydrogen bonding formed between 3′-O and 4′-H makes 3′-OH as the active site which is supported by its bond dissociation energy values. The computed values of the adiabatic ionization potential, electron affinity, hardness, softness, electronegativity and electrophilic index indicate that orientin possess good radical scavenging activity. In this study, role of molecular electrostatic potential and electron density distribution map in predicting the importance of B-ring are analyzed and reported. Spin density distribution analysis for the radicals is formed by summing of spin on rings A, B and C. The most active system able to transfer a hydrogen atom is orientin compared to vitexin and the bond dissociation enthalpy follows the order benzene>ethyl acetate>water.

Effect of a π-spacer between a donor and an acceptor on small molecule-based data-storage device performance

We demonstrate that replacing the hydrazone linkage by a linear π-spacer bridging a carbazole donor and a naphthalimide acceptor induces a critical change in molecular organization and electron density distribution in the conjugation backbone that correlates with a remarkable variation of memory performance from DRAM to WORM types.

Symmetry interplay in Brownian photomotors: From a single-molecule device to ensemble transport

Unlike most of Brownian motor models in which the state of a point particle is described by a single scalar fluctuating parameter, we consider light-induced dichotomic fluctuations of electron density distributions in an extended molecule moving in the electrostatic periodic potential of a polar substrate. This model implies that the potential energy profiles of two motor states differ substantially and their symmetry is dictated by the interplay between the symmetries of the substrate potential and of molecular electronic states. As shown, a necessary condition for the occurrence of directed motion, the asymmetry of the potential energy profiles, is satisfied for (i) symmetric electron density distributions in molecules on asymmetric substrates and (ii) asymmetric electron density distributions in molecules on symmetric substrates. In the former case, the average velocity of directed motion is independent of molecular orientations and the ensemble of molecules moves as a whole, whereas in the latter case, oppositely oriented molecules move counterdirectionally thus causing the ensemble to diffuse. Using quantum chemical data for a specific organic-based photomotor as an example, we demonstrate that the behavior of molecular ensembles is controllable by switching on/off resonance laser radiation: they can be transported as a whole or separated into differently oriented molecules depending on the ratio of symmetric and antisymmetric contributions to the substrate electrostatic potential and to the molecular electron density distributions.

Transmission of Electronic Substituent Effects through a Benzene Framework: A Computational Study of 4-Substituted Biphenyls Based on Structural Variation

The transmission of substituent effects through a benzene framework has been studied by a novel approach, based on the structural variation of the Ph group in p-Ph-C(6)H(4)-X molecules. The molecular structures of many 4-substituted biphenyls were determined from MO calculations at the HF/6-31G* and B3LYP/6-311++G** levels of theory. The twist angle between the phenyl probe (ring B) and the benzene framework carrying the substituent (ring A) was set at 90° to prevent π-electron transfer from one ring to the other and at 0° to maximize it. The structural variation of the probe is best represented by a linear combination of the internal ring angles, termed S(F)(BIPH(o)) and S(F)(BIPH(c)) for the orthogonal and coplanar conformations of the molecules, respectively. Regression analysis of these parameters using appropriate explanatory variables reveals a composite field effect, a substantial proportion of which is originated by resonance-induced π-charges on the carbon atoms of ring A. Field-induced polarization of the π-system of ring A also contributes to the structural variation of the probe. Thus, the S(F)(BIPH(o)) parameter is very well reproduced by a linear combination of the π-charges on the ortho, meta, and para carbons of ring A, an uncommon example of a quantitative relationship between molecular geometry and electron density distribution. Comparison of S(F)(BIPH(o)) with the gas-phase acidities of para-substituted benzoic acids shows that, while the deprotonating carboxylic probe is more sensitive to π-electron withdrawal than donation, the phenyl probe is equally sensitive to both. While the ability of the orthogonal biphenyl system to exchange π-electrons with the para substituent is the same as that of the benzene ring in Ph-X molecules, an increase by about 18% occurs when the conformation is changed from orthogonal to coplanar. The structural variation of the probe becomes more complicated, however. This is due to π-electron transfer from one ring to the other, which is shown to introduce quadratic terms in the regressions.

Group II metal complexes with the N-(2-oxy-3,5-di-tert-butylphenyl)-4,6-di-tert-butyl-o-iminobenzoquinone ligand: an ESR study

The Group II metal (Mg, Ca, Sr, Ba, Zn, Cd) complexes based on the paramagnetic N-(2-oxy-3,5-di-tert-butylphenyl)-4,6-di-tert-butyl-o-iminobenzoquinone ligand were generated in solutions and studied by ESR spectroscopy. The magnesium, zinc, and cadmium complexes with trialkylphosphine ligands were prepared. Their molecular structures and electron density distribution were studied by ESR spectroscopy and DFT calculations.