Local Ionization Energy Research Articles

Synthesis, crystal structure analysis, spectral investigations, DFT computations and molecular dynamics and docking study of 4-benzyl-5-oxomorpholine-3-carbamide, a potential bioactive agent

4-benzyl-5-oxomorpholine-3-carbamide has been synthesized; single crystals were grown by slow evaporation solution growth technique at room temperature and characterized by single crystal X-ray diffraction, FT-IR, FT-Raman and 1H-NMR. The compound crystallizes in the monoclinic space group P21/n. The molecular geometry of the compound was optimized by using Density Functional Theory (DFT/B3LYP) method with 6–311++G(d,p) basis set in the ground state and geometric parameters are in agreement with the X-ray analysis results of the structure. The experimental vibrational spectra were compared with the calculated spectra and each vibrational wave number was assigned on the basis of potential energy distribution (PED). The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbital's (HOMOs) and lowest unoccupied molecular orbital's (LUMOs). Besides molecular electrostatic potential (MEP), frontier molecular orbital's (FMOs), some global reactivity descriptors, thermodynamic properties, non-linear optical (NLO) behavior and Mullikan charge analysis of the title compound were computed with the same method in gas phase, theoretically. Potential reactive sites of the title compound have been identified by average local ionization energy and Fukui functions, both mapped to the electron density surface. Bond dissociation energies for all single acyclic bonds have been calculated in order to investigate autoxidation and degradation properties of the title compound. Atoms with pronounced interactions with water molecules have been detected by calculations of radial distribution functions after molecular dynamics simulations. The experimental results are compared with the theoretical calculations using DFT methods for the fortification of the paper. Further the docking studies revealed that the title compound as a docked ligand forms a stable complex with pyrrole inhibitor with a binding affinity value of −7.5 kcal/mol. This suggests that the title compound might exhibit inhibitory activity against pyrrole inhibitor. To confirm the potential practical applicability of the title compound antimicrobial activity was tested against gram negative and gram positive bacteria.

Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole

Antimicrobial active 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole (NATPB) was synthesized and observed IR, Raman bands are compared with the theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number splits into a doublet with a noted difference and is red shifted from the computed value, which indicates the weakening of NH bond resulting in proton transfer to the neighbouring oxygen atom. The HOMO-LUMO plots reveal the charge transfer in the molecular system through the conjugated paths. The electrophilic and nucleophilic reactive sites are identified from the MEP plot. Mapping of average local ionization energy (ALIE) values to the electron density surface served us as a tool for prediction of molecule sites possibly prone to electrophilic attacks. Other important reactive centres of the title molecule were detected by calculations of Fukui functions. Calculations of bond dissociation energies (BDE) for hydrogen abstraction were used in order to assess whether the NATPB molecules is prone to autoxidation mechanism or not, while BDE of the remaining single acyclic bonds were used in order to determine the weakest bond. Interaction properties with water were investigated by molecular dynamics (MD) simulations and calculations of radial distribution functions (RDFs). The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations (MICs) ranging between 32 and 128 μg/ml. The compound exhibited significant antibacterial activity (32 μg/ml) against an antibiotic resistant E. faecalis isolate, at same potency with the compared standard drugs vancomycin and gentamycin sulfate. The molecular docking studies show that the compound might exhibit inhibitory activity against CDK inhibitors.

Local Electron Attachment Energy and Its Use for Predicting Nucleophilic Reactions and Halogen Bonding.

A new local property, the local electron attachment energy [E(r)], is introduced and is demonstrated to be a useful guide to predict intermolecular interactions and chemical reactivity. The E(r) is analogous to the average local ionization energy but indicates susceptibility toward interactions with nucleophiles rather than electrophiles. The functional form E(r) is motivated based on Janak's theorem and the piecewise linear energy dependence of electron addition to atomic and molecular systems. Within the generalized Kohn-Sham method (GKS-DFT), only the virtual orbitals with negative eigenvalues contribute to E(r). In the present study, E(r) has been computed from orbitals obtained from GKS-DFT computations with a hybrid exchange-correlation functional. It is shown that E(r) computed on a molecular isodensity surface, ES(r), reflects the regioselectivity and relative reactivity for nucleophilic aromatic substitution, nucleophilic addition to activated double bonds, and formation of halogen bonds. Good to excellent correlations between experimental or theoretical measures of interaction strengths and minima in ES(r) (ES,min) are demonstrated.

Vibrational spectroscopic analysis of cyanopyrazine-2-carboxamide derivatives and investigation of their reactive properties by DFT calculations and molecular dynamics simulations

Using density functional theory technique in the B3LYP approximation and cc-pVDZ (5D, 7F) basis set, the molecular structural parameters and vibrational wave numbers of two cyanopyrazine-2-carboxamide derivatives have been investigated. On the basis of potential energy distribution detailed vibrational assignments of observed FT-IR and FT-Raman bands have been proposed. Using molecular electrostatic potential map relative reactivities towards electrophilic and nucleophilic attack are predicted. The first and second hyperpolarizabilities are calculated and the first hyperpolarizability of the title compounds are greater than that of the standard NLO material urea. Molecular studies reveal that the predicted binding affinities of the best poses were −8.7 kcal/mol for BACPC, −9.0 kcal/mol for CBACPC, and −8.8 kcal/mol for the original inhibitor. Efforts were made in order to investigate local reactivity properties of title compounds as well. In order to do so we have calculated average local ionization energy (ALIE) surfaces, Fukui functions, bond dissociation energies (BDE) (within the framework of DFT calculations) and radial distribution functions (RDF) (within the molecular dynamics simulations). ALIE surfaces and Fukui functions gave us initial information on the site reactivity towards electrophilic and nucleophilic attacks. BDE indicated locations that might be prone to autoxidation mechanism, while RDF indicated which atoms of title molecules are having pronounced interactions with water.

Theoretical investigation of loratadine reactivity in order to understand its degradation properties: DFT and MD study.

Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding their fundamental reactive properties. In this study we have theoretically investigated reactive properties of LOR using both density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT study is used for collecting information related to the molecule stability, structure, frontier molecular orbitals, quantum molecular descriptors, charge distribution, molecular electrostatic potential surfaces, charge polarization, and local reactivity properties according to average local ionization energy surfaces. Based on these results, N24 atom of pyridine ring and oxygen atom O1 were identified with nucleophilic nature. In order to collect the information necessary for the proposition of degradation compounds we also calculated bond dissociation energies (BDE) for hydrogen abstraction and single acyclic bonds as well. According to BDE, the oxidation is likely to occur in the piperidine and cycloheptane rings. MD simulations were used in order to understand the interactions with water through radial distribution functions (RDF). Based on RDFs the most important interactions with solvent are determined for carbon atom C5, chlorine atom Cl15, and oxygen atom O1. Collected results based on DFT calculations and MD simulations provided information important for suggestion of possible degradation compounds. Covalent and noncovalent interactions between LOR and (•)OH have also been investigated.

Reactive, spectroscopic and antimicrobial assessments of 5-[(4-methylphenyl) acetamido]-2-(4-tert-butylphenyl)benzoxazole: Combined experimental and computational study

The synthesis, FT-IR, FT-Raman and NMR spectral analysis of an antimicrobial active benzoxazole derivative, 5-[(4-methylphenyl)acetamido]-2-(4-tert-butylphenyl) benzoxazole (MPATB) is reported. The localization of HOMO, LUMO plots in the title compound over the title molecule shows the charge transfer in the molecular system through the conjugated paths.The electrophilic and nucleophilic sites are revealed from the molecular electrostatic potential map. The first hyperpolarizability of the title compound is greater than that of the standard nonlinear optical material urea and the title compound and its derivatives are good objects for further research in nonlinear optical analysis. Molecule sites prone to electrophilic attacks have been detected by calculation of average local ionization energies, while calculations of Fukui functions have provided additional information about the local reactivity properties. Bond dissociation energies have been calculated in order to investigate autoxidation possibilities of the title molecule, as well as to determine the weakest bonds and therefore the sites where process of degradation could start. Reactive properties with water have been investigated by molecular dynamics simulations and calculations of radial distribution functions. The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations ranging between 8 and 128 μg/ml. The compound exhibited significant antifungal activity (64 μg/ml) against Candida krusei, at same potency with the compared standard drugs fluconazole. The docked title compound forms a stable complex with thymidylate synthase and got a binding affinity value of −8.5 kcal/mol and the title compound can be a lead compound for developing new anti-cancerous drug.

Synthesis, XRD crystal structure, spectroscopic characterization (FT-IR, 1H and 13C NMR), DFT studies, chemical reactivity and bond dissociation energy studies using molecular dynamics simulations and evaluation of antimicrobial and antioxidant activities of a novel chalcone derivative, (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic system with P21/c space group with the unit cell parameters of a = 16.147 (2) Å, b = 14.270 (2) Å, c = 5.9058 (9) Å, β = 92.577 (3)° and Z = 4. The molecular geometry obtained from X-Ray structure determination was optimized by Density Functional Theory (DFT) using B3LYP/6-31G+(d, p)/Lanl2dz(f) method in the ground state. The IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. In order to investigate local reactivity properties of the title molecule, we have conducted DFT calculations of average local ionization energy surface and Fukui functions which were mapped to the electron density surface. In order to predict the open air stability and possible degradation properties, within DFT approach, we have also calculated bond dissociation energies. 1H and 13C NMR spectra were recorded and chemical shifts were calculated theoretically and compared with the experimental values. In addition, in vitro antimicrobial results show that the title compound has great potential of antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis and Micrococcus luteus bacteria and antifungal activity against Candida albicans in comparison to some reported chalcone derivatives. Antioxidant studies revealed the highest metal chelating activity of this compound.

Generalized average local ionization energy and its representations in terms of Dyson and energy orbitals.

Ryabinkin and Staroverov [J. Chem. Phys. 141, 084107 (2014)] extended the concept of average local ionization energy (ALIE) to correlated wavefunctions by defining the generalized ALIE as Ī(r)=-∑jλj|fj(r)|(2)/ρ(r), where λj are the eigenvalues of the generalized Fock operator and fj(r) are the corresponding eigenfunctions (energy orbitals). Here we show that one can equivalently express the generalized ALIE as Ī(r)=∑kIk|dk(r)|(2)/ρ(r), where Ik are single-electron removal energies and dk(r) are the corresponding Dyson orbitals. The two expressions for Ī(r) emphasize different physical interpretations of this quantity; their equivalence enables one to calculate the ALIE at any level of ab initio theory without generating the computationally expensive Dyson orbitals.

Molecular conformational analysis, reactivity, vibrational spectral analysis and molecular dynamics and docking studies of 6-chloro-5-isopropylpyrimidine-2,4(1H,3H)-dione, a potential precursor to bioactive agent

FT-IR and FT-Raman spectra of 6-chloro-5-isopropylpyrimidine-2,4(1H,3H)-dione were recorded and analyzed. The vibrational wavenumbers were computed using DFT quantum chemical calculations and the data obtained from wavenumber calculations are used to assign the experimentally obtained bands. Potential energy distribution was done using GAR2PED software. The geometrical parameters of the title compound are in agreement with the XRD results. NBO analysis, frontier molecular orbital and first and second hyperpolarizability and molecular electrostatic potential results are also reported. The possible electrophile attacking sites of the title compound is identified using MEP surface plot study. Molecule sites prone to electrophilic attacks were identified using average local ionization energy surfaces, while further insight into the local reactivity properties of the title molecule has been gained by calculation of Fukui functions. Intra-molecular non-covalent interactions have been detected and visualized. Degradation properties based on autoxidation and hydrolysis have been investigated by calculation of bond dissociation energies and radial distribution functions, respectively. From the molecular docking study, the ligand binds at the active site of the substrate by weak non-covalent interactions and amino acids Leu89 forms alkyl interaction with the CH3 groups and Glu90 amino acid forms π-anion interaction with the pyrimidine ring and Thr369 and Ser366 amino acids form H-bond interaction with the CO and NH group, respectively. From the conformational analysis, the calculated structures show that the C6C9C10 angle in the most stable form is about 8° smaller compared to the C8C9C10 angle, indicating a higher repulsive force between the (CH3)2HC– moiety and the chlorine atom due to the size of chlorine compared to oxygen atoms.

Determination of reactive properties of 1-butyl-3-methylimidazolium taurate ionic liquid employing DFT calculations

Reactive properties of a newly synthesized third generation ionic liquid, namely the 1-butyl-3-methylimidazolium taurate ([BMIM][Tau]), has been investigated employing density functional theory (DFT) calculations. M06-2X exchange-correlation functional with 6-31G+(d,p) basis set was chosen for the geometrical optimizations and calculation of various properties. Global reactive properties have been investigated using molecular orbital theory and quantum molecular descriptors. Dipole moment indicates weaker interactions with water than in the case of our previously investigated [BMIM][Sal] ionic liquid (IL). Further, molecular electrostatic potential (MEP) and averaged local ionization energy (ALIE) surfaces recognized nitrogen atom of [Tau]− and carbon atoms of imidazolium ring to be prone to electrophilic attacks. Fukui functions provided further insight into the local reactivity properties of this IL, indicating that C(9) position of imidazolium ring (in some literature as C2) could be prone to the nucleophilic attacks, while other carbon atoms of imidazolium ring could be prone to electrophilic attacks. Bond dissociation energies (BDEs) have been calculated as well, indicating that SO bond of [Tau]− could be vulnerable to chemical species, however, our previous molecular dynamics results indicate that this part of the molecule has pronounced interaction with water, so the hydrolysis mechanism is more probable. Finally, using all calculated data we summarized reactive properties.

FT-IR, FT-Raman and NMR characterization of 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate and investigation of its reactive and optoelectronic properties by molecular dynamics simulations and DFT calculations

The FT-IR and FT-Raman spectra of the synthesized compound, 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate is recorded and analyzed. Optimized molecular structure, wave numbers, corresponding assignments regarding 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate has become screened tentatively as well as hypothetically using Gaussian09 program package. Natural bonding orbital assessment has been completed with a reason to clarify charge transfer or conjugative interaction, the intra-molecular re-hybridization and delocalization of electron density within the molecule. The NMR spectral assessment had been made choosing structure property relationship by chemical shifts along with the magnetic shielding effects regarding the title compound. The first and second hyperpolarizabilities were calculated. The calculated first order hyperpolarizability is commensurate with the documented worth of very similar derivatives and could be an interesting object for more experiments on nonlinear optics. Local reactivity properties have been investigated using average local ionization energies and Fukui functions. Investigation of optoelectronic properties encompassed calculations of reorganization energies and hopping rates of charge carriers within the framework of Marcus semi-empiric approach. The docked ligand title compound forms a stable complex with CDK inhibitors and gives a binding affinity value of −9.7 kcal/mol and molecular docking results suggest that the compound might exhibit inhibitory activity against CDK inhibitors.

Regioselectivity of third-row maingroup dicarbides, C2X (X = K-Br) for CO interaction: Fukui function and topological analyses

In this work, we present our calculations, based on density functional theory (DFT) to explore chemical reactivity of C2X (X=K-Br) towards CO molecule. Computed condensed Fukui function (f-) reveals the carbon atom of C2X (X=K-Br) to be the most active site for the CO interaction. This fact is also confirmed by the comparatively lesser average local ionization energy (I(r)¯) for the active carbon atom. Bader’s topological parameters such as electron density ρ>0.30a.u. with negative ∇2ρ and HBCP (total energy density) at the bond BCP of the carbon atoms of both C2X (X=K-Br) and CO infers the CO interaction in all the cases to be of shared-kind.

Origin of static and dynamic steps in exact Kohn-Sham potentials

Knowledge of exact properties of the exchange-correlation (xc) functional is important for improving the approximations made within density functional theory. Features such as steps in the exact xc potential are known to be necessary for yielding accurate densities, yet little is understood regarding their shape, magnitude and location. We use systems of a few electrons, where the exact electron density is known, to demonstrate general properties of steps. We find that steps occur at points in the electron density where there is a change in the `local effective ionization energy' of the electrons. We provide practical arguments, based on the electron density, for determining the position, shape and height of steps for ground-state systems, and extend the concepts to time-dependent systems. These arguments are intended to inform the development of approximate functionals, such as the mixed localization potential (MLP), which already demonstrate their capability to produce steps in the Kohn-Sham potential.

Coordination compounds of a hydrazone derivative with Co(iii), Ni(ii), Cu(ii) and Zn(ii): synthesis, characterization, reactivity assessment and biological evaluation

Increasing inhibitory effect of Zn-Hp2DAP < Hp2DAP < Co-Hp2DAP on ABC transporter MDR1 drug efflux pump.

Functionalization of single-walled (n,0) carbon and boron nitride nanotubes by carbonyl derivatives (n = 5, 6): a DFT study

By using density functional theory calculations, the chemical functionalization of finite-sized (5,0) and (6,0) carbon nanotubes (CNTs) and boron nitride nanotubes (BNNTs) by different carbonyl derivatives –COX (X = H, CH3, OCH3, OH, and NH2) is studied in terms of geometrical and electronic structure properties. Also, the benefits of local reactivity descriptors is studied to characterize the reactive sites of the external surface of the tubes. These local reactivity descriptors include the electrostatic potential VS(r) and average local ionization energy ĪS(r) on the surfaces of these nanotubes. The estimated ĪS(r) values show that the functionalized CNTs tend to activate the surface toward electrophilic/radical attack. Results show that the chemical functionalization of CNTs leads to the reduction of VS(r) values and therefore enhances the surface reactivity. On the other hand, BNNTs resist chemical functionalization due to the negligible decrease in the VS,min and ĪS,min values. Generally, in contrast to BNNTs, the chemical functionalization of CNTs can considerably improve their surface reactivity. To verify the surface reactivity pattern based on the chosen reactivity descriptors, the reaction energies for the interaction of an H + ion or hydrogen radical with external surface of the functionalized CNTs and BNNTs are calculated. A general feature of all studied systems is that stronger potentials are associated with regions of higher curvature.

DFT study of 1-butyl-3-methylimidazolium salicylate: a third-generation ionic liquid.

A detailed theoretical investigation of the third-generation ionic liquid (IL) 1-butyl-3-methylimidazolium salicylate ([BMIM][Sal]), performed within the framework of density functional theory (DFT), is presented in this paper. The B3LYP-D3, M06-2X, and M06-2X-D3 functionals were used to obtain the equilibrium geometries of the two ions [BMIM](+) and [Sal](-). It is shown that the equilibrium ion geometries obtained with the dispersion-corrected B3LYP functional are very close to the ion geometries obtained with the M06-2X and M06-2X-D3 functionals. Global reactivity was assessed using molecular orbital theory and quantum molecular descriptors. Molecular electrostatic potential (MEP) surfaces and average local ionization energy (ALIE) surfaces were created in order to elucidate the charge distribution and reactivity of the investigated IL. Ion-pair binding energies were calculated with all three functionals, and the results confirmed the presence of a strong electrostatic interaction between the ions, while further insight into the interactions between the two ions was obtained by analyzing noncovalent interactions based on the reduced density gradient (RDG) surface, which revealed a total of nine interactions between the ions. Finally, the aromaticity of each ion was investigated by calculating the nucleus-independent chemical shift (NICS) parameter, which indicated that significant changes in the charge delocalization on each ion occur when the two ions interact.

A simple method for the determination of the Tolman electronic parameter of different phosphorus containing ligands, by means of the average local ionization energy

The average local ionization energy (I(r)) was tested as a theoretical descriptor of the Tolman electronic parameter (TEP) for a set of monodentate phosphines and phosphites. Results indicated that this magnitude correlates with the experimental TEP, which could be explained in terms of the HSAB principle of Pearson. This function represents a simple, reliable, and fast option to measure the electronic contribution of these type of compounds. The performance of the electrostatic potential (V(r)) was also studied for these molecules. Comparison of I(r) with the experimental basicity showed that this magnitude, as well as the experimental TEP correlate with the reported pKb values, which in both cases are poor. A simple methodology to measure the Tolman cone angle from the mapping of the I(r) function over the van der Waals isocontour is also described.

A multi-agent quantum Monte Carlo model for charge transport: Application to organic field-effect transistors

We have developed a multi-agent quantum Monte Carlo model to describe the spatial dynamics of multiple majority charge carriers during conduction of electric current in the channel of organic field-effect transistors. The charge carriers are treated by a neglect of diatomic differential overlap Hamiltonian using a lattice of hydrogen-like basis functions. The local ionization energy and local electron affinity defined previously map the bulk structure of the transistor channel to external potentials for the simulations of electron- and hole-conduction, respectively. The model is designed without a specific charge-transport mechanism like hopping- or band-transport in mind and does not arbitrarily localize charge. An electrode model allows dynamic injection and depletion of charge carriers according to source-drain voltage. The field-effect is modeled by using the source-gate voltage in a Metropolis-like acceptance criterion. Although the current cannot be calculated because the simulations have no time axis, using the number of Monte Carlo moves as pseudo-time gives results that resemble experimental I/V curves.

Understanding the Highly Varying pKa of Arylamines. A Perspective from the Average Local Ionization Condensed-to-Atom Framework.

The highly varying experimental pKa values for 36 arylamines spanning 7 orders of magnitude is carefully examined. Within this framework, a valence condensed-to-atom model for the average ionization energy is introduced and tested. The theoretical approach is connected to orbital Fukui functions directly mapped into semilocal or regional site-specific responses. It is revealed that the average local ionization energies associated with the amino nitrogen atom is linearly correlated to the basicity of the substituted arylamines, properly reproducing the experimental ordering of basicity. The condensed-to-atom descriptor exhibits a high predictive power, providing a new direct reactivity evaluation of significant value.

Two Aromatic Rings Coupled a Sulfur-Containing Group to Favor Protein Electron Transfer by Instantaneous Formations of π∴S:π↔π:S∴π or π∴π:S↔π:π∴S Five-Electron Bindings.

The cooperative interactions among two aromatic rings with a S-containing group are described, which may participate in electron hole transport in proteins. Ab initio calculations reveal the possibility for the formations of the π∴S:π↔π:S∴π and π∴π:S↔π:π∴S five-electron bindings in the corresponding microsurrounding structures in proteins, both facilitating electron hole transport as efficient relay stations. The relay functionality of these two special structures comes from their low local ionization energies and proper binding energies, which varies with the different aromatic amino acids, S-containing residues, and the arrangements of the same aromatic rings according to the local microsurroundings in proteins.