Electrostatic Potential Map Analysis Research Articles

The adsorption of CO gas on the surface of boron nitride incorporating 2D carbon allotropes: a DFT analysis

The adsorption properties of different Carbon allotropes (i.e., graphene, γ-graphyne, Mobius graphene, and R-graphyne) and their corresponding Boron (N) and Nitrogen (N) incorporated BCN nanostructures toward carbon monoxide (CO) gas are studied via density functional theory calculation. All the adsorbents demonstrated negative formation energies and real frequencies, i.e., can be synthesized and have dynamical stability. The adsorption energies have increased due to B and N incorporation, although still comparatively low for practical application. The highest adsorption energy with suitable recovery time is observed for the Mobius BCN structure, about −0.112 eV and 77.8 ps, respectively. Very nominal charge transfer is observed via Mulliken charge distribution and electrostatic potential map analysis. The changes in energy gap and electrical conductivity are observed due to CO adsorption.

Molecular Modeling Studies of β-Sitosterol Extract from Miconia burchellii Triana (Melastomataceae) from Brazilian Cerrado

The Brazilian Cerrado biome is considered one of the 25 hotspots worldwide that contain bioactive compounds due to its great biodiversity; however, the reduction of its native area over time due to the expansion of urbanization and agribusiness may have compromised knowledge of its biological variety. In this context, knowledge about Cerrado species can contribute to its biodiversity preservation. This study aims to describe the isolation, molecular architecture and theoretical calculations of the compound (3S,8S,9S,10R,13R,14S,17R)-17-[(2R,5R)-5-ethyl -6-methylheptan-2-yl]-10,13 dimethyl 2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro1H-cyclopenta[a]phenanthren-3-ol, extracted from the Brazilian Cerrado Miconia burchellii plant. The supramolecular arrangement was described by Hirshfeld surface analysis, demonstrating the intermolecular interactions in the crystalline packing. The structure-property relationship shows the electrostatic potential map analysis, which reveals that the oxygen region is susceptible to electrophilic attack, and the frontier molecular orbital confirmed the kinetic stability of this compound. This study represents another step forward in the knowledge of compounds with pharmacological and medicinal properties extracted from the Cerrado.

Analysis of the Comparative Growth Kinetics of Paenarthrobacter ureafaciens YL1 in the Biodegradation of Sulfonamide Antibiotics Based on Substituent Structures and Substrate Toxicity

The high consumption and emission of sulfonamide antibiotics (SAs) have a considerable threat to humans and ecosystems, so there is a need to develop safer and more effective methods than conventional strategies for the optimal removal of these compounds. In this study, four SAs with different substituents, sulfadiazine (SDZ), sulfamerazine (SMR), sulfamethoxazole (SMX), and sulfamethazine (SMZ) were removed by a pure culture of Paenarthrobacter ureafaciens YL1. The effect of the initial SAs concentration on the growth rate of strain YL1 was investigated. The results showed that the strain YL1 effectively removed various SAs in the concentration range of 0.05–2.4 mmol·L−1. The Haldane model was used to perform simulations of the experimental data, and the regression coefficient of the model indicated that the model had a good predictive ability. During SAs degradation, the maximum specific growth rate of strain YL1 was ranked as SMX > SDZ > SMR > SMZ with constants of 0.311, 0.304, 0.302, and 0.285 h−1, respectively. In addition, the biodegradation of sulfamethoxazole (SMX) with a five-membered substituent was the fastest, while the six-membered substituent of SMZ was the slowest based on the parameters of the kinetic equation. Also, density functional theory (DFT) calculations such as frontier molecular orbitals (FMOs), and molecular electrostatic potential map analysis were performed. It was evidenced that different substituents in SAs can affect the molecular orbital distribution and their stability, which led to the differences in the growth rate of strain YL1 and the degradation rate of SAs. Furthermore, the toxicity of P. ureafaciens is one of the crucial factors affecting the biodegradation rate: the more toxic the substrate and the degradation product are, the slower the microorganism grows. This study provides a theoretical basis for effective bioremediation using microorganisms in SAs-contaminated environments.

Unexpected role of two ortho-OH groups for the hydrogenation of CO2 to methanol catalyzed by Fe bipyridinol complexes

A density functional theory study of Fe-catalyzed hydrogenation of CO2 to methanol reveals an unexpected metal–ligand cooperation mechanism with two ortho-OH groups play key roles for the breaking of C–O and O–H bonds and formation of O–H…O hydrogen bonds. The formation of methanediol via hydride transfer from Fe to formic acid (4′ → TS6,7) is the rate-determining step with a total barrier of 30.8 kcal mol−1 in free energy. Furthermore, by replacing the two meta (R1) and two para (R2) hydrogen atoms in the bipyridinol ligand and the coordinated CN and CO with different functional groups, we built a series of stable iron complexes and computationally predicted their catalytic activities for hydrogenation of CO2 to methanol. Among all newly proposed iron complexes, 1t and 1u are promising catalyst candidates for hydrogenation of CO2 to methanol with rather low total free energy barriers of 26.6 and 28.8 kcal mol−1, respectively. The electrostatic potential map analysis indicates that stronger electron donating ligands on iron may lead to higher catalytic activities.

Density functional theoretical study, spectroscopic characterization and molecular docking of the diuretic drug, spironolactone, adsorbed on AuNPs surface and in-vitro studies based on anticancer activity studies against A549 lung cancer cell line

In this study, the geometry, intramolecular charge transfer interactions, and harmonic vibrational frequencies of the diuretic drug, Spironolactone (SPL) and SPL adsorbed on gold nanoparticle (SPLA molecule) were investigated with the help of density functional theory method. Both molecules were found to be stabilized by intramolecular hydrogen bonds C7-H37. O27 and C16-H47. O2, as well as intramolecular charge transfer interactions. These interactions were quantitatively confirmed using natural localized molecular orbitals (NLMOs) analysis. The frontier molecular orbital analysis provided a comparative picture of the reactivity, showing a low value of the energy gap, revealing electron transport in the molecule. The most reactive sites of the molecules were predicted by the molecular electrostatic potential map analysis together with the study of local and global reactivity descriptors. FT-IR and Raman spectral analysis confirmed the existence of significant hydrogen bonding, and charge delocalization in the molecules. Molecular docking performed for the biological activity screening of both molecules along with the SERS and MTT assay (in vitro) analysis confirmed their cancer activity. All the comparative results lead to the conclusion that SPLA possess enhanced therapeutic activity than SPL and hence can be used for effective label-free monitoring of cells in-vitro.

Synthesis, growth, DFT, and HOMO-LUMO studies on pyrazolemethoxy benzaldehyde single crystals

Pyrazolemethoxy benzaldehyde (PMB) was synthesized and crystals were grown by slow evaporation solution growth method. PMB was crystallized in a monoclinic crystal system with a centrosymmetric C2/c space group, according to single-crystal X-ray diffraction analysis. The crystalline planes were identified using powder X-ray diffraction analysis. FTIR - FT-Raman spectroscopic techniques were performed to determine the vibrational modes of functional groups for the grown crystal. UV-visible spectral analysis and photoluminescence studies were taken to investigate the linear optical properties of the grown crystal. Thermogravimetric and differential thermal analysis (TG/DTA) were used to determine the thermal stability of the PMB crystal. In addition to this density functional theory (DFT) calculations such as frontier molecular orbital's (FMOs), global chemical reactivity parameters, hyperpolarizability, natural bond orbital (NBO) analysis, Mullikan atomic charge distribution, and molecular electrostatic potential map analysis were carried out in gaseous phase using B3LYP/6-311G* basis set.

Spectroscopic and density functional theory (DFT) approach of zwitterionic 4-aminobenzenesulfonic acid for optoelectronic applications

In this present study, a coupled experimental and density functional theory (DFT) studies of organic nonlinear optical (NLO) material, 4-aminobenzenesulfonic acid (4AB), is reported. By slow evaporation method the optical quality, single crystals of 4AB were developed under aqueous medium condition. Single-crystal XRD analysis reveals the crystalline nature of 4AB crystal; the 4AB crystal structure is in the orthorhombic system with noncentrosymmetric (NCS), Pca21, space group. The morphology of developed crystal has been indexed and showed a major facet of the crystal as (002). The molecular construction of 4AB has been well established using 13C and 1H NMR spectroscopic studies. FTIR and FT-RAMAN were found out to be the corresponding vibrational modes of 4AB. Linear optical studies of grown crystal allow near-UV cut-off wavelength range at 261 nm with good optical transparency in the visible and near-IR region and exhibited ultraviolet wavelength emission. Thermal analysis revealed a high thermal stability value of 288 °C for 4AB crystal. Moreover, dielectric and photoconductivity investigations were accomplished efficiently and revealed low dielectric constant and positive photoconducting nature, respectively. The molecular structure of 4AB was optimized at the B3LYP/cc-pVTZ basis set using density functional theory (DFT). The intermolecular hydrogen bond (N1–H1···O1) formation was confirmed by the Mulliken atomic charge distribution analysis and molecular electrostatic potential map analysis. Frontier molecular orbitals (FMOs) evidenced the lower energy gap for the 4AB molecule. Besides NLO properties, the dipole moment (µ0), polarizability (α) and first-order hyperpolarizability (β) were measured for the optimized 4AB molecule.

TMPE Derived from Saffron Natural Monoterpene as Cytotoxic and Multidrug Resistance Reversing Agent in Colon Cancer Cells.

Terpenes constitute one of the largest groups of natural products. They exhibit a wide range of biological activities including antioxidant, anticancer, and drug resistance modulating properties. Saffron extract and its terpene constituents have been demonstrated to be cytotoxic against various types of cancer cells, including breast, liver, lung, pancreatic, and colorectal cancer. In the present work, we have studied anticancer properties of TMPE, a newly synthesized monoterpene derivative of β-cyclocitral—the main volatile produced by the stigmas of unripe crocuses. TMPE presented selective cytotoxic activity to doxorubicin-resistant colon cancer cells and was identified to be an effective MDR modulator in doxorubicin-resistant cancer cells. Synergy between this derivative and doxorubicin was observed. Most probably, TMPE inhibited transport activity of ABCB1 protein without affecting its expression level. Analysis of TMPE physicochemical parameters suggested it was not likely to be transported by ABCB1. Molecular modeling showed TMPE being more reactive molecule than the parental compound—β-cyclocitral. Analysis of electrostatic potential maps of both compounds prompted us to hypothesize that reduced reactivity as well as susceptibility to electrophilic attack were related to the lower general toxicity of β-cyclocitral. All of the above pointed to TMPE as an interesting candidate molecule for MDR reversal in cancer cells.

Vibrational spectroscopic characterization, quantum chemical and molecular docking studies of Valyl-Methionine dipeptide

In this study, valyl-methionine dipeptide (Val-Met), a breakdown product of protein digestion or protein catabolism,has been investigated both theoretically and experimentally. Four different valyl-methionine conformations were formed, using the geometric parameters of two asymmetric units of L-Valine and L-Methionine, taken from the literature and their optimized geometric parameters were obtained by DFT/B3LYP level of theory, using different basis sets. The vibrational spectral analysis for the obtained two energetically most stable conformations were carried out theoretically by using 6-311++G(d,p) basis set. Experimental vibrational spectra of the title molecule were compared with the calculated spectra and the vibrational modes were assigned on the basis of potential energy distributions (PED) analysis, performed using the MOLVIB program. Furthermore, molecular electrostatic potential map analysis was carried out and dipole moment of the compound was calculated. Conformation analysis is an important step in molecular modeling. The selection of suitable conformers for many flexible drug molecules, which can be present in many conformations by turning around single bonds, to adopt different conformations, can easily be overlooked. In this work a series of dipeptide with A and B forms of valine and methionine amino acids have been chosen as examples to demonstrate the importance of conformational analysis. Energy differences between conformations underline the importance of a detailed conformational analysis and should be taken into account when defining their activities. Results show that the formation of hydrogen bonds between N1 and H17 and between H17 and O25 in Valyl(B)-Methionine(B) dipeptide, affects the stability of the molecule. The molecular electrostatic potential of the title molecule has also been calculated which is a very useful property in prediction of molecular reactive behavior. In addition, in silico molecular docking studies were performed for the title molecule with DNA. The results indicated the ability of the Val-Met dipeptide to bind DNA.

Efficient Mediation of Electron Transfer Pathway by Quadrupolar Interactions: The Constitutional, Electronic and Energetic Complementarities in Supramolecular Chemistry

SummaryOur knowledge on the chemistry across molecular and supramolecular levels is insufficient. Here, we show that inclusion of a guest molecule through quadrupolar interactions leads to a chemical transformation of the molecular system. With covalently bonded dimolybdenum complex units as the electron donor (D) and acceptor (A) and a thienylene group (C4H2S) as the bridge (B), the mixed-valence D-B-A complexes are shaped with clefts in the middle of the molecule. The D-A electron transfer is optically studied under the Marcus-Hush theoretic framework. It is found that in aromatic solvents, the electronic coupling matrix elements (Hab) and electron transfer rate constants (ket) are dramatically reduced. DFT calculations and electrostatic potential map analysis indicate that in the solution, an aromatic molecule is encapsulated in the cleft of the D-B-A array; quadrupole-quadrupole interaction between the guest molecule and the C4H2S group evokes charge redistribution, which increases the HOMO-LUMO energy gap, intervening in the through-bond electron transfer. These results demonstrate that a supramolecular system is unified underlying the characteristics of the assembled molecules through constitutional, electronic and energetic complementarities, thus, sharing the general principles developed in molecular chemistry. This study illustrates the role of site-specific interactions of the aromatic residues in biological systems in governing the charge transfer processes.

Reactivity of 12-tungstophosphoric acid and its inhibitor potency toward Na+/K+-ATPase: A combined 31P NMR study, ab initio calculations and crystallographic analysis

Influence of 12-tungstophosphoric acid (WPA) on conversion of adenosine triphosphate (ATP) to adenosine diphosphate (ADP) in the presence of Na+/K+-ATPase was monitored by 31P NMR spectroscopy. It was shown that WPA exhibits inhibitory effect on Na+/K+-ATPase activity. In order to study WPA reactivity and intermolecular interactions between WPA oxygen atoms and different proton donor types (D=O, N, C), we have considered data for WPA based compounds from the Cambridge Structural Database (CSD), the Crystallographic Open Database (COD) and the Inorganic Crystal Structure Database (ICSD). Binding properties of Keggin's anion in biological systems are illustrated using Protein Data Bank (PDB). This work constitutes the first determination of theoretical Bader charges on polyoxotungstate compound via the Atom In Molecule theory. An analysis of electrostatic potential maps at the molecular surface and charge of WPA, resulting from DFT calculations, suggests that the preferred protonation site corresponds to WPA bridging oxygen. These results enlightened WPA chemical reactivity and its potential biological applications such as the inhibition of the ATPase activity.

Synthesis, growth, characterization and quantum chemical investigations of a promising organic nonlinear optical material: Thiourea-glutaric acid

A promising organic nonlinear optical (NLO) material of thiourea-glutaric acid (TG) has been synthesized and its single crystals were grown by a conventional slow evaporation method. The molecular structure of TG was explored by (1H and 13C) NMR spectral and single crystal X-ray diffraction (SCXRD) techniques. The vibrational modes of functional groups involved in TG crystal were ascertained profoundly using FTIR and FT-Raman spectroscopic techniques. The grown crystal exhibited a high optical transmittance of 65% within the range of 226–1100 nm. Thermal stability was determined as 236 °C for TG crystal using thermogravimetric/differential thermal analysis (TG/DTA) and differential scanning calorimetric (DSC). Second harmonic efficiency (SHG) of TG was about 6.2 times higher than the standard KDP crystal. The surface of TG crystal showed high tolerance to the laser power with the threshold value of 3.5 GW/cm2. The dielectric study revealed that grown TG crystal showed a low dielectric constant (ɛr = 18) and a low dielectric loss values at higher frequencies. The mechanical and photoconducting behaviours of TG crystal were studied intensely. Furthermore, density functional theory (DFT) calculations such as Mulliken atomic charge distribution, frontier molecular orbital (FMOs), molecular electrostatic potential map analysis and NLO calculations were carried out.

Synthetic studies of centromere-associated protein-E (CENP-E) inhibitors: 1.Exploration of fused bicyclic core scaffolds using electrostatic potential map

Centromere-associated protein-E (CENP-E), a mitotic kinesin that plays an important role in mitotic progression, is an attractive target for cancer therapeutic drugs. For the purpose of developing novel CENP-E inhibitors as cancer therapeutics, we investigated a fused bicyclic compound identified by high throughput screening, 4-oxo-4,5-dihydrothieno[3,4-c]pyridine-6-carboxamide 1a. Based on this scaffold, we designed inhibitors for efficient binding at the L5 site in CENP-E utilizing homology modeling as well as electrostatic potential map (EPM) analysis to enhance CENP-E inhibitory activity. This resulted in a new lead, 5-bromoimidazo[1,2-a]pyridine 7, which showed potent CENP-E enzyme inhibition (IC50: 50nM) and cellular activity with accumulation of phosphorylated histone H3 in HeLa cells. Our homology model and EPM analysis proved to be useful tools for the rational design of CENP-E inhibitors.

Geometrical criteria versus quantum chemical criteria for assessment of intramolecular hydrogen bond (IMHB) interaction: A computational comparison into the effect of chlorine substitution on IMHB of salicylic acid in its lowest energy ground state conformer

Density functional theory based computational study has been performed to characterize intramolecular hydrogen bonding (IMHB) interaction in a series of salicylic acid derivatives varying in chlorine substitution on the benzene ring. The molecular systems studied are salicylic acid, 5-chlorosalicylic acid, 3,5-dichlorosalicylic acid and 3,5,6-tricholorosalicylic acid. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇2ρ(r) at the bond critical point using atoms-in-molecule theory. Topological features, energy densities based on ρ(r) through perturbing the intramolecular H-bond distances suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of covalent interaction. The interplay between aromaticity and resonance-assisted hydrogen bonding (RAHB) is discussed using both geometrical and magnetic criteria as the descriptors of aromaticity. The optimized geometry features, molecular electrostatic potential map analysis are also found to produce a consensus view in relation with the formation of RAHB in these systems.

Synthesis, molecular and crystal structure analysis of 2-bromo-4-chloro-6-{[4-(3-methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-hydrazonomethyl}-phenol by experimental methods and theoretical calculations

A novel hydrazone derivative 2-bromo-4-chloro-6-{[4-(3-methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-hydrazonomethyl}-phenol was synthesized and characterized by IR, UV–Vis spectroscopy and X-ray single crystal diffraction. The compound crystallizes in monoclinic space group P21/c with a=8.0862(3)Å, b=7.6168(1)Å, c=37.3168(12)Å and β=91.186(1)°. In addition, the molecular geometry and vibrational frequencies of the title compound in ground state have been calculated by using density functional theory (DFT) at B3LYP level with 6-31G and 6-31G(d,p) basis sets. The geometrical parameters of the title compound obtained from XRD studies are in good agreement with the calculated values. The analysis of IR spectrum supported by DFT calculations was particularly devoted to the manifestations of hydrogen bonding in the νstr(NH) and νstr(OH) vibrations. To determine the conformational flexibility for a selected torsion angle τ(C6C1C7N1) one-dimensional potential energy scan was performed using AM1 in the full range of 0–360° increasing of 10°. UV–Vis absorption spectrum of the compound has been compared to theoretical spectrum (vertical excitations) computed by time dependent density functional theory (TD-DFT). Besides frontier molecular orbitals and molecular electrostatic potential map analysis were investigated by theoretical calculations.

Vibrational investigation, molecular orbital studies and molecular electrostatic potential map analysis on 3-chlorobenzoic acid using hybrid computational calculations

The FT-IR and FT-Raman spectra of 3-chlorobenzoic acid (3CBA) are recorded in the liquid state. The fundamental vibrational frequencies, intensity of vibrational bands and the optimized geometrical parameters of the compound are evaluated using HF and DFT (LSDA/B3LYP/B3PW91/MPW1PW91) methods with 6-311+G(d,p) basis set. The theoretical wave numbers are scaled down and compared with the experimental values which showed very good agreement. Comparison of stimulated spectra with the experimental spectra provides important information about the ability of the hybrid computational method to describe the vibrational modes. The HOMO, LUMO, chemical hardness ( η), chemical potential ( μ), electrophilicity values ( ω) and maximum amount of electronic charge transfer (Δ N max) are calculated. The molecular electrostatic potential (MESP) is calculated and the corresponding graphs are drawn. Some thermodynamic parameters and physico-chemical properties are calculated and discussed.

Characterization of pyridoxal phosphate as an optical label for measuring electrostatic potentials in proteins

This paper presents data which allow one to characterize pyridoxal 5′-phosphate (PLP) as an optical label for electrostatic potential measurements in proteins. Experimental studies were carried out with 6- N-(5′-phosphopyridoxyl)-2- N-acetyl-lysyl methyl ester (PLP-ALME) as a model compound which simulates PLP covalently bound to a protein. Calculations of electrostatic potential maps were done using the model compound 2,4-dimethyl-3-hydroxy-5-hydroxymethyl phosphate-pyridine (DHHPP). Studies on relative changes in PLP-ALME fluorescence and absorbance vs. pH resulted in four p K a values of PLP-ALME in solution which can be used as intrinsic p K a values (p K int) of the ionizable groups of the label covalently bound to the protein. The p K a values obtained from fluorescence data are 4.1, 5.6, 8.7 and 11.1 and those from absorbance data are 3.1, 4.7, 8.7 and 11.0. The differences between corresponding p K a values are related to differences in PLP-ALME behaviour between the excited and ground electronic states and to intramolecular charge-charge interactions. Quenching of PLP-ALME fluorescence by I −, acrylamide and Cs + at pH 6, 7 and 8 shows that in the case of I − and acrylamide the Stern-Volmer constants of quenching ( K sv) decrease with increasing pH, while the opposite is true for K sv of Cs +. These results as well as the analysis of electrostatic potential maps of DHHPP show that with its ampholytic character PLP can be used to measure local electrostatic potentials in the pH range 5–9.