Understanding the effects of building block rings of π electron-rich organic photocatalysts in CO2 transformation to amino acids.

Understanding the effective factors in the performance of some Oligo (p-phenylenes) (OPPs) and Polycyclic Aromatic Hydrocarbons (PAHs), as efficient organocatalysts in photocatalytic CO2 transformations are the main goals of this investigation. The studies are based on density functional theory (DFT) calculations on the mechanistic aspects of C-C bond formation through a coupling reaction between CO2•- and amine radical. The reaction is performed through two successive single electron transfer steps. After careful kinetic investigations by Marcus' theory rules, powerful descriptors are used to describe the behavior of observed barrier energies of electron transfer steps. The studied PAHs and OPPs consist of different numbers of rings. Thus, it can be considered different charge densities, afforded from π electrons, of PAHs and OPPs that cause distinguished efficiency in kinetic aspects of electron transfer steps. Electrostatic Surface Potential (ESP) analyses reveal a good relationship between the charge density of the studied organocatalysts in single electron transfer (SET) steps and the kinetic parameters of the steps. Moreover, the contribution of rings in the framework of PAHs and OPPs would be another effective factor in the barrier energies of SET steps. Aromatic properties of the rings, studied by the Anisotropy of the Current-Induced Density (ACID), Nucleus-Independent Chemical Shift (NICS), the multi-center bond order (MCBO), and AV1245 Indexes, are the other impressive factors in the role of rings in SET steps. The results show that the aromatic properties of the rings are not similar to each other. Higher aromaticity affords remarkable reluctance of the corresponding ring to participate in SET steps.

A molecular dynamic study on the ability of phosphorene for designing new sensor for SARS-CoV-2 detection.

Due to the dramatic increase in the number of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), designing new selective and sensitive sensors for the detection of this virus is of importance. In this research, by employing full atomistic molecular dynamics (MD) simulations, the interactions of the receptor-binding domain (RBD) of the SARS-CoV-2 with phosphorene and graphene nanosheets were analyzed to investigate their sensing ability against this protein. Based on the obtained results, the RBD interactions with the surface of graphene and phosphorene nanosheets do not have important effects on the folding properties of the RBD but this protein has unique dynamical behavior against each nanostructure. In the presence of graphene and phosphorene, the RBD has lower stability because due to the strong interactions between RBD and these nanostructures. This protein spreads on the surface and has lower structural compaction, but in comparison with graphene, RBD shows greater stability on the surface of the phosphorene nanosheet. Moreover, RBD forms a more stable complex with phosphorene nanosheet in comparison with graphene due to greater electrostatic and van der Waals interactions. The calculated Gibbs binding energy for the RBD complexation process with phosphorene and graphene are -200.37 and -83.65 kcal mol-1, respectively confirming that phosphorene has higher affinity and sensitivity against this protein than graphene. Overall, the obtained results confirm that phosphorene can be a good candidate for designing new nanomaterials for selective detection of SARS-CoV-2.

A theoretical approach on the ability of functionalized gold nanoparticles for detection of Cd2.

Cadmium (Cd) as a toxic element that is widely present in water, soil, and air has important effects on human health, therefore proposing an accurate and selective method for detection of this element is of importance. In this article, by employing full atomistic molecular dynamics (MD) simulations and density functional theory dispersion corrected (DFT-D3) calculations, the effects of 6-mercaptonicotinic acid (MNA) and L-cysteine (CYS) on the stability of gold nanoparticles (AuNPs) and their sensitivity against Cd2+ were investigated. The obtained results indicate that pure AuNPs are not stable in water, while functionalized AuNPs with CYS and MNA groups have considerable stability without aggregation. In other words, the functional groups on the surface of AuNPs elevate their resistance against aggregation by an increase in the repulsive interactions between the gold nanoparticles. Moreover, functionalized AuNPs have considerable ability for selective detection of Cd2+ in the presence of different metal ions. Based on the MD simulation results, MNA-CYS-AuNPs (functionalized AuNPs with both functional groups) have the maximum sensitivity against Cd2+ in comparison with MNA-AuNPs and CYS-AuNPs due to the strong electrostatic interactions. DFT-D3 calculations reveal that the most probable interactions between the metal ions and functional groups are electrostatic, and Cd2+ can aggregate functionalized AuNPs due to strong electrostatic interactions with MNA and CYS groups. Moreover, charge transfer and donor-acceptor analyses show that molecular orbital interactions between the functional groups and Cd2+ can be considered as the driving force for AuNPs aggregation. A good agreement between the theoretical results and experimental data confirms the importance of the molecular modeling methods as a fast scientific protocol for designing new functionalized nanoparticles for application in different fields.

Recent advances in computational methods for biosensor design.

Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.

Theoretical Design of Functionalized Gold Nanoparticles as Antiviral Agents against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

In this research, through the use of molecular dynamics (MD) simulations, the ability of gold nanoparticles (AuNPs) functionalized by different groups, such as 3-mercaptoethylsulfonate (Mes), undecanesulfonic acid (Mus), octanethiol (Ot), and a new peptide, to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated. According to the crystal structure of angiotensin-converting enzyme 2 (ACE2), which binds to the SARS-CoV-2 receptor binding domain (RBD), 15 amino acids of ACE2 have considerable interaction with RBD. Therefore, a new peptide based on these amino acids was designed as the functional group for AuNP. On the basis of the obtained results, functionalized AuNPs have remarkable effects on the RBD and strongly interact with this protein of SARS-CoV-2. Among the studied nanoparticles, the AuNP functionalized by new peptide forms a more stable complex with RBD in comparison with ACE2, which is the human receptor for SARS-CoV-2. Different analyses confirm that the designed AuNPs can be good candidates for antiviral agents against COVID-19 disease.

Theoretical study on the absorption of carbon dioxide by DBU-based ionic liquids.

In this article, 20 ns molecular dynamic (MD) simulations and density functional theory (DFT) were used to investigate the absorption of CO2 molecules by some functionalized 1,8-diazabicyclo[5,4,0]-udec-7-ene (DBU)-based ILs. According to the MD results, the highest coordination number for NC is observed in the case of [DBUH+][Im-], which indicates that the functionalization of the imidazole anion by different alkyl groups decreases the interaction ability of the anion with CO2 molecules. The addition of water molecules to the ILs decreases the ability of the anion to interact with CO2 because of the hydrogen bond formation between the imidazole anions and water. Two different paths were proposed for CO2 absorption by the ILs, and the effect of alkyl groups on the kinetics and thermodynamics of the reaction was analyzed by using the M06-2X functional at the 6-311++G(d,p) level of theory in the gas phase and water. On the basis of the results, CO2 absorption is more favorable in [DBUH+][Im-], thermodynamically. Kinetic parameters show that the alkylation of the imidazole anion by ethyl, propyl, iso-propyl, and phenyl groups decreases the rate of CO2 absorption, because of the steric and electron-withdrawing effect of different alkyl groups. In the presence of water molecules, the lowest activation Gibbs energy is related to [DBUH+][Im-], which confirms the greater ability of this IL in CO2 absorption.

A DFT study on the metal ion selectivity of deferiprone complexes.

In this work, systematic density functional theory (DFT) calculations were performed to study the interactions of various metal ions (Al3+, Fe3+, Co2+, Ni2+, Cu2+, and Zn2+) and the clinically useful chelating agent called deferiprone (DFP) at the M05-2X/6-31G(d) level of theory. The thermodynamic parameters of metal-deferiprone complexes were determined in water. Based on the obtained data, the theoretical binding energy trend is as follows: Al3+ > Fe3+ > Cu2+ > Ni2+ > Co2+ > Zn2+, confirming that [Al(DFP)3] has the most interaction energy. Moreover, Natural bond orbital analysis was employed to determine and analyze the natural charges on different atoms and charge transfer between the metal ions and ligands (oxygen atoms) as well as the interaction energy (E(2)) values. The calculated value of Æ©E(2) (donor-acceptor interaction energy) for [Al(DFP)3] complex is higher than other complexes, which is according to energy analysis. To confirm the type of effective interactions and bonding properties in the water, the quantum theory of atoms in molecules (QTAIM) analysis was applied. QTAIM analysis confirmed that the strongest M - O bond is found in the [Al(DFP)3] complex. The calculated topological properties at the bond critical points, such as the ratio of the kinetic energy density to the potential energy density, -G(r)/V(r), electronic energy density, H(r), confirm that M - O bonds in the Al-deferiprone complex are non-covalent, while in other complexes, they are electrostatic and partially covalent.

The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study.

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb2+ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb2+ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb2+. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb2+. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb2+. The density functional theory (DFT) results show that Pb2+ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb2+. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb2+. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma.

Evaluation and understanding the performances of various derivatives of carbonyl-stabilized phosphonium ylides in CO2 transformation to cyclic carbonates.

The kinetic and mechanism evaluations of the formation of cyclic carbonates by carbonyl-stabilized phosphonium ylides as an efficient and new class of organocatalysts are the main purposes of this research. Recently, it has been reported that tetraarylphosphonium salts play the role of organocatalysts in carbon dioxide conversion to cyclic carbonates. However, in this research, the oxygen atom of the carbonyl-stabilized phosphonium ylides was treated as the nucleophilic atom for the carbon dioxide activation. Two probable mechanisms were considered and analyzed by the energetic span model. The kinetic behavior of the carbonyl-stabilized phosphonium ylides in the carbon dioxide or ethylene oxide activation was justified by the molecular electrostatic potential (ESP) analysis at the nuclear position. However, it was confirmed that the activation strain model (ASM) was a more efficient tool in explaining the kinetic behaviors in the carbon dioxide or ethylene oxide activation. A change in the ESP value of the donor-acceptor interacting system (ΔΔVn) and distortion energy at the transition states (ΔEstrain(ζ)) were the outcomes of the ESP and ASM models, respectively, which showed a linear correlation. The electron localization function (ELF) concept was used to justify the kinetic behavior of the second step of the preferred mechanism, revealing that the electron-donating/withdrawing groups substituted on the organocatalysts have a remarkable effect on the electron density of the involved basin at the transition states. On the basis of different analyses, it was proposed that carbonyl-stabilized phosphonium ylides having electron-donating substituents are the best candidates for carbon dioxide conversion to cyclic carbonates.

The first coordination polymers with an [O]2[N]P(S)-Hg segment: a combined experimental, theoretical and database study.

The study of one-dimensional coordination polymers {Hg2Cl4L1}n (1), {HgBr2L1}n (2) and {Hg2Cl4L2}n (3) (L1 = (S)P(OC2H5)2NHC6H4NHP(S)(OC2H5)2 and L2 = (S)P(OC2H5)2NC4H8NP(S)(OC2H5)2) is the first such structural study of Hg(ii) coordination polymers with (O)2(N)PS-based ligands. The mercury atoms adopt a distorted trigonal pyramidal environment, Hg(Cl)3(S) for 1 and 3 and Hg(Br)2(S)2 for 2, and the difference observed in the stoichiometry of mercury halide to the thiophosphoramide ligand in 1 and 3 with respect to the one in 2 is a result of the formation of the Hg2Cl2 ring, however, the molar ratio 2 : 1 of HgX2 (X = Cl and Br) to ligand was used for the preparation of all three complexes. The strengths of mercury-sulfur and mercury-halide covalent bonds are evaluated by theoretical calculations (QTAIM and NBO) which show their principally electrostatic nature with a partial covalent contribution. The energies of interactions building supramolecular assemblies and intramolecular interactions, i.e. NHCl, NHBr, CHCl, CHBr, CHO, CHS and CHπ, are theoretically evaluated. The characteristic structural features arising from the aromatic/aliphatic linkers in the ligands and chloride/bromide attached to mercury are investigated by Hirshfeld surface analysis and fingerprint plots.

A simple paper-based aptasensor for ultrasensitive detection of lead (II) ion.

In this study, a simple paper-based aptasensor has been developed for the ultrasensitive detection of lead (Pb2+) ion within about 10 min. The aptasensor has been successfully designed by taking advantages of the Förster Resonance Energy Transfer (FRET) process and the super fluorescence quenching property of graphene oxide (GO) sheet. The sensing mechanism of the aptasensor is based on the conformational switch of the Pb2+-specific aptamer from a random coil to a G-quadruplex structure. An injection of Pb2+ on the paper-based platform induces the release of the specific aptamer from the GO surface that recovers the fluorescence emission. Under the optimal experimental conditions, there is a good linear relationship between the fluorescence recovery and the Pb2+concentration in the ranges of 5-70 pM and 0.07-20 nM. Moreover, the aptasensing array exhibits a high sensitivity to Pb2+ with an ultra-low detection limit of 0.5 pM. The developed aptasensor has been successfully applied to determine Pb2+ in tap water, lake water, milk, and human blood serum. The paper-based aptasensor can be efficiently utilized to detect other metal ions and biological molecules by substituting target specific aptamer.

Solvent Effects on Intra-/Intermolecular Charge Transfer in Indoloquinoxaline-Based Dyes.

In this work, kinetics and dynamics of the functionality of indoloquinoxaline-based dye-sensitized solar cells (DSSCs), QX22-QX25, were investigated in gas and solvent media. Quantum chemistry properties of the dyes at the excited states show that each moiety of the (D)2-A-π-A system has a specific effect on the photovoltaic properties. Solvent effect analysis shows that among ethanol, toluene, tetrahydrofuran, and methylene dichloride, toluene is the preferred medium for intra-/intermolecular charge transfer, dynamically and kinetically. Moreover, the behavior of the light harvesting efficiency (LHE) and incident photon-to-current efficiency (IPCE) are not similar, due to a strong effect of the Gibbs energy of electron injection on the energy conversion efficiency. Finally, the dye composed of -COOH as the anchoring group and thiophene as the π-spacer is the best candidate to be applied in DSSC due to its better efficiency originated from a lower electrophilicity and electronic chemical potential.

Aptasensors as the future of antibiotics test kits-a case study of the aptamer application in the chloramphenicol detection.

Antibiotics are a type of antimicrobial drug with the ubiquitous presence in foodstuff that effectively applied to treat the diseases and promote the animal growth worldwide. Chloramphenicol as one of the antibiotics with the broad action spectrum against Gram-positive and Gram-negative bacteria is widely applied for the effective treatment of infectious diseases in humans and animals. Unfortunately, the serious side effects of chloramphenicol, such as aplastic anemia, kidney damage, nausea, and diarrhea restrict its application in foodstuff and biomedical fields. Development of the sufficiently sensitive methods to detect chloramphenicol residues in food and clinical diagnosis seems to be an essential demand. Biosensors have been introduced as the promising tools to overcome the requirement. As one of the newest types of the biosensors, aptamer-based biosensors (aptasensors) are the efficient sensing platforms for the chloramphenicol monitoring. In the present review, we summarize the recent achievements of the accessible aptasensors for qualitative detection and quantitative determination of chloramphenicol as a candidate of the antibiotics. The present chloramphenicol aptasensors can be classified in two main optical and electrochemical categories. Also, the other formats of the aptasensing assays like the high performance liquid chromatography (HPLC) and microchip electrophoresis (MCE) have been reviewed. The enormous interest in utilizing the diverse nanomaterials is also highlighted in the fabrication of the chloramphenicol aptasensors. Finally, some results are presented based on the advantages and disadvantages of the studied aptasensors to achieve a promising perspective for designing the novel antibiotics test kits.

Evaluation of N-H...S and N-H...π interactions in O,O'-diethyl N-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies.

In the crystal structure of O,O'-diethyl N-(2,4,6-trimethylphenyl)thiophosphate, C13H22NO2PS, two symmetrically independent thiophosphoramide molecules are linked through N-H...S and N-H...π hydrogen bonds to form a noncentrosymmetric dimer, with Z' = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06-2X level within the 6-311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N-H...S hydrogen bond is slightly stronger than the N-H...π hydrogen bond. This is reflected in differences between the calculated N-H stretching frequencies of the isolated molecules and the frequencies of the same N-H units involved in the different hydrogen bonds of the hydrogen-bonded dimer. For these hydrogen bonds, the corresponding charge transfers, i.e. lp (or π)→σ*, were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.

Carbon Dioxide Absorption by the Imidazolium-Amino Acid Ionic Liquids, Kinetics, and Mechanism Approach.

The kinetics and mechanism of CO2 absorption by ionic liquids (ILs) were studied, theoretically. The studied ILs are composed of 1-ethyl-3-methylimidazolium [Emim]+ as the cation with a general formula of the [Emim][X] (X = Gly-, Ala-, Lys-, Arg-). To investigate the alkyl chain length and the number of the amine group effects on the CO2 absorption, different amino acid anions were chosen. On the basis of the enthalpy changes during CO2 capture, a chemisorption nature is confirmed. An increase in the number of amine (-NH2) groups in the ILs structures, facilitates the CO2 absorption. According to kinetic results, the rate of CO2 absorption by [Emim][Gly] is higher than that of [Emim][Ala]. This can be interpreted by a higher steric hindrance in [Emim][Ala] due to an additional methyl group in the amino acid chain. Donor-acceptor interactions and C-N bond formation were investigated by natural bond orbital analysis. Moreover, topological studies show a covalent nature for the C-N bond critical point that showing CO2 capture is a chemisorption process. Finally, on the basis of kinetic energy results, donor-acceptor interaction and topological analysis, [Emim][Arg] is proposed as the best candidate for CO2 absorption from the kinetic and thermodynamic viewpoints.

Antioxidant activity of selenenamide-based mimic as a function of the aromatic thiols nucleophilicity, a DFT-SAPE model.

The mechanism of action of the selenenamide 1 as a mimic of the glutathione peroxidase (GPx) was investigated by the density functional theory. The solvent-assisted proton exchange procedure was applied to model the catalytic behavior and antioxidant activity of this mimic. To have an insight into the charge transfer effect, different aromatic thiols, including electron donating substituents on the phenyl ring were considered. The catalytic behavior of the selenenamide was modeled in a four-step mechanism, described by the oxidation of the mimic, the reduction of the obtained product, selenoxide, the reduction of the selenenylsulfide and dehydration of selenenic acid. On the basis of the activation parameters, the final step of the proposed mechanism is the rate determining states of the catalytic cycle. Turnover frequency (TOF) analysis showed that the electron donating groups at the para-position of the phenyl ring of the PhSH do not affect the catalytic activity of the selenenamide in contrast to p-methyl thiophenol which indicates the highest nucleophilicity. The evaluation of the electronic contribution of the various donating groups on the phenyl ring of the aromatic thiols shows that the antioxidant activity of the selenenamide sufficiently increases in the presence of the electron-donating substitutions. Finally, the charge transfer process at the rate-determining state was investigated based on the natural bond orbital analysis.

A review on modified carbon materials as promising agents for hydrogen storage.

Carbon materials have been regarded as promising agents for hydrogen storage because of properties such as their light weight, acceptable affinity of carbon for hydrogen and high specific surface area. We can identify many different carbon materials which have been studied extensively such as activated carbons (AC) graphene sheets (GS), carbon nanotubes (CNTs) and other derivative carbon materials derived from theoretical and experimental methods such as g-C3N4, graphyne and carbon nanolayer. These materials can be modified by additional ingredients like free metals, metal oxides, and alloys to improve their hydrogen storage capacity. In this short review article, we attempt to introduce new, reliable, complete and categorised data for researchers concentrating on articles from the last five years (2013-2017) relating to hydrogen storage.

DFT investigation on the selective complexation of Fe3+ and Al3+ with hydroxypyridinones used for treatment of the aluminium and iron overload diseases.

The chelating agents for Al3+ and Fe3+ metal cations with therapeutic applications have been considered in the recent years. In designing of the hydroxypyridinones (HPOs) as the therapeutic chelating agents for iron and aluminium overload pathologies, quantum mechanical (QM) calculations are necessary for predicting the binding energies and thermodynamic parameters of the metal-HPO complexes. Three derivatives of the HPOs called 3-hydroxy-1,2-dimethylpyridin-4(1H)-one (DFP), 3-hydroxy-4(1H)-pyridinone (HOPO) and 5-hydroxy-2-(hydroxymethyl)pyridin-4(1H)-one (P1) were investigated for complexation with Fe3+ and Al3+ metal ions. Because of the maximum interaction between Fe3+ and HPOs, all HPOs form stable complexes with Fe3+ metal ion. Moreover, it was found that [Fe-P1]2+ is a more stable complex than [Fe-DFP]2+ and [Fe-3,4-HOPO]2+ in the gas phase and water, confirming that P1 is the strongest selective iron chelator. The more stability of [Fe-P1]2+ was attributed to an intramolecular hydrogen bond formation between the hydrogen atom of NH group and the oxygen atom of CH2OH chain. All complexes of the HPOs with Fe3+ and Al3+ were formed through the oxygen atoms of the CO and OH groups of the HPO. Natural bond orbital analysis showed that the interaction of the lone pair electrons of the oxygen atom of the chelator and antibonding orbitals of the Al3+ and Fe3+ are important in the complex formation. Topological parameters at the bond critical points confirmed the effective interaction between the Al3+ and Fe3+ metal ions and HPO as well as the nature of the metal-oxygen bonds.

Molecular dynamic simulation and DFT study on the Drug-DNA interaction; Crocetin as an anti-cancer and DNA nanostructure model.

In this research, the interaction of Crocetin as an anti-cancer drug and a Dickerson DNA has been investigated. 25 ns molecular dynamic simulations of Crocetin and DNA composed of 12 base pairs and a sequence of d(CGCGAATTCGCG)2 were done in water. Three definite parts of the B-DNA were considered in analyzing the best interactive site from the thermodynamic point of view. Binding energy analysis showed that van der Waals interaction is the most important part related to the reciprocal O and H atoms of the Crocetin and DNA. Stabilizing interactions, obtained by ΔG calculations, showed that maximum and minimum interactions are related to the S1 and S3 regions, respectively. This means that the most probable van der Waals interaction site of the Dickerson B-DNA and Crocetin is located in the minor groove of DNA. Two sharp peaks at 2.55 and 1.75 Å in radial distribution functions of the PO⋯HO and NH⋯OC parts are related to new hydrogen bonds between the Crocetin and DNA in the complex which can be considered as the driving force of the anti-cancer mechanism of the Crocetin. Average values of 0.3 au and zero for the electron densities of the H⋯O bonds for DNA and complex, obtained by Quantum theory of atoms in molecules (QTAIM), means that the origin of DNA instability after complexation may be related to the H-bond denaturation by Crocetin. Finally, the evaluation of the dispersion interactions using the dispersion functional, -148.76 kcal.mol-1, confirmed the importance of the dispersion interaction in drug-DNA complex.

Computational Kinetic Modeling of the Catalytic Cycle of Glutathione Peroxidase Nanomimic: Effect of Nucleophilicity of Thiols on the Catalytic Activity.

The catalytic cycle of a new derivative of ebselen, 1, was elucidated via three steps by the density functional theory and solvent-assisted proton exchange procedure involving indirect proton exchange through a hydrogen-bonded transfer network. Different behaviors of the aromatic and aliphatic thiols were investigated in the reduction of selenoxide (step 2 → 3) and selenurane (step 3 → 1) based on their nucleophilicity. The reduction of selenoxide in the presence of thiophenol (ΔG‡ = 15.9 kcal·mol-1) is faster than that of methanethiol (ΔG‡ = 29.3 kcal·mol-1), and methanethiol makes the reduction of selenoxide unspontaneous and kinetically unfavorable (ΔG = 2.8 kcal·mol-1). The nucleophilic attack may be enhanced by using the thiophenol backbone at the selenium center to lower the energy barrier of the selenoxide reduction (ΔG‡ = 15.9 kcal·mol-1). On the basis of the turnover frequency calculations, during the catalytic cycle, the rate of the reaction was analyzed and discussed. Low values of the electron density and Laplacian at the transition states are the evidence of the covalent O-H and O-O bonds rupture in the presence of methanethiol and thiophenol. The nature of the critical bond points was characterized, using the quantum theory of atoms in molecules, based on the electron location function and localized orbital locator values. Finally, the charge transfer process at the rate-determining step was investigated based on the natural bond orbital analysis.