Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study

Hydration reactions of two anticancer Pt(IV) complexes JM149 and JM216 (Satraplatin) were studied computationally together with the hydration of the Pt(II) complex JM118, which is a product of the Satraplatin reduction. Thermodynamic and kinetic parameters of the reactions were determined at the B3LYP/6-311++G(2df.2pd)//B3LYP/6-31 + G(d)) level of theory. The water solution was modeled using the COSMO implicit solvation model, with cavities constructed using Klamt’s atomic radii. It was found that hydration of the Pt(IV) complexes is an endergonic/endothermic reaction. It follows the (pseudo)associative mechanism is substantially slower (k?≈?10^-11 s^?1) than the corresponding reaction of Pt(II) analogues ((k?≈?10^-5 s^?1). Such a low value of the reaction constant signifies that the hydration of JM149 and Satraplatin is with high probability a kinetically forbidden reaction. Similarly to JM149 and Satraplatin, the hydration of JM118 is an endothermic/endoergic reaction. On the other hand, the kinetic parameters are similar to those of cisplatin Zimmermann et al. (J Mol Model 17:2385–2393, 2011), allowing the hydration reaction to occur at physiological conditions. These results suggest that in order to become active Satraplatin has to be first reduced to JM118, which may be subsequently hydrated to yield the active species.

Structural characterization of the (MeSH)4 potential energy surface

A random walk on the PES for (MeSH)₄ clusters produced 50 structural isomers held together by hydrogen-bonding networks according to calculations performed at the B3LYP/6–311++G** and MP2/6–311++G** levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted.

DFT studies of the adsorption and dissociation of H2O on the Al13 cluster: origins of this reactivity and the mechanism for H2 release

A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculations revealed that the H₂O molecule is easily adsorbed onto the Al₁₃ surface, forming adlayers. The dissociation of the first H₂O molecule from the bimolecular H₂O structure via the Grotthuss mechanism is the most kinetically favorable among the five potential pathways for O–H bond breaking. The elimination of H₂ in the reaction of an H₂O molecule with a hydrogen atom on the Al cluster via the Eley–Rideal mechanism has a lower activation barrier than the elimination of H₂ in the reaction of two adsorbed H atoms or the reaction of OH and H. Following the adsorption and dissociation of H₂O, the structure of Al₁₃ is distorted to varying degrees.

A B3LYP and MP2(full) theoretical investigation into the strength of the C-NO2 bond upon the formation of the molecule-cation interaction between Na+ and the nitro group of nitrotriazole or its methyl derivatives

The changes of bond dissociation energy (BDE) in the C–NO₂ bond and nitro group charge upon the formation of the molecule-cation interaction between Na⁺ and the nitro group of 14 kinds of nitrotriazoles or methyl derivatives were investigated using the B3LYP and MP2(full) methods with the 6-311++G**, 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The strength of the C–NO₂ bond was enhanced in comparison with that in the isolated nitrotriazole molecule upon the formation of molecule-cation interaction. The increment of the C–NO₂ bond dissociation energy (ΔBDE) correlated well with the molecule-cation interaction energy. Electron density shifts analysis showed that the electron density shifted toward the C-NO₂ bond upon complex formation, leading to the strengthened C-NO₂ bond and the possibly reduced explosive sensitivity.

Density functional investigation of CO adsorption on Ni-doped single-walled armchair (5,5) boron nitride nanotubes

The adsorption of CO onto Ni-doped boron nitride nanotubes (BNNTs) was investigated using density functional theory at the B3LYP/LanL2DZ level of theory. The structures of the Ni-doped BNNTs and their CO-adsorbed configurations were obtained. It was found that the strength of adsorption of CO onto Ni-doped perfect BNNTs is higher than that on defective BNNTs. The electronic properties of all of the adsorption configurations of CO on Ni-doped BNNTs are reported.

Microsolvation and hydration enthalpies of CaC2O4(H2O) n (n = 0-16) and C2O4 2-(H2O) n (n = 0-14): an ab initio study

We studied hydrated calcium oxalate and its ions at the restricted Hartree–Fock RHF/6-31G* level of theory. Performing a configurational search seems to improve the fit of the HF/6-31G* level to experimental data. The first solvation shell of calcium oxalate contains 13 water molecules, while the first solvation shell of oxalate ion is formed by 14 water molecules. The first solvation shell of Ca(II) is formed by six water molecules, while the second shell contains five. At 298.15 K, we estimate the asymptotic limits (infinite dilution) of the total standard enthalpies of hydration for Ca(II), oxalate ion and calcium oxalate as ?480.78, –302.78 and –312.73 kcal mol^?1, resp. The dissociation of hydrated calcium oxalate is an endothermic process with an asymptotic limit of +470.84 kcal mol^?1.

Investigation of the antioxidant properties of hyperjovinol A through its Cu(II) coordination ability

Hyperjovinol A (2-methyl-1-(2,4,6-trihydroxy-3-(3-hydroxy-3,7-dimethyloct-6-enyl)phen yl)propan-1-one) is an acylated phloroglucinol isolated from Hypericum Jovis and exhibiting antioxidant properties comparable with those of the most common antioxidant drugs. The study models the compound’s antioxidant ability through its ability to coordinate a Cu²⁺ ion and reduce it to Cu⁺. Complexes with a Cu²⁺ ion were calculated for all the low energy and for representative high energy conformers of hyperjovinol A, placing the ion in turn near each of the electron-rich binding sites. The most stable complexes are those in which Cu²⁺ binds simultaneously to the O of the OH in the geranyl-type chain (R′) and the C═C double bond at the end of R′, or to the O of a phenol OH and the O of the OH in R′. The most stable complexes in which Cu²⁺ binds only to one site are those in which it binds to the C═C double bond at the end of R′ or to the sp² O of the COCH(CH₃)₂ acyl group. Cu²⁺ is reduced to Cu⁺ in all complexes. Comparisons with corresponding complexes of other molecular structures in which one or more of the structural features of hyperjovinol A are modified attempt to elucidate the role, for the antioxidant ability, of relevant features of hyperjovinol A, like the presence and position of the OH or the C═C double bond in R′. Calculations at the DFT/B3LYP/6–31+G(d,p) level were performed for all the structures considered. Calculations utilizing the LANL2DZ pseudopotential for the Cu²⁺ ion were also performed for hyperjovinol A.

Theoretical study of geometrical and nonlinear optical properties of pyridinum N-phenolate betaine dyes

This paper presents an ab initio quantum chemical investigation of the geometrical structures and the non-linear optical properties (NLO) of three structural isomers of pyridinium N-phenolate betaine dye. The ground state geometrical parameters and the first-order hyperpolarizabilities were calculated using the Hartree-Fock (HF) as well as the second-order perturbation Møller-Pleset (MP2) method with the 6–31G, 6–31G(d), 6–31G(d,p), 6–31+G(d), 6–31++G(d,p), 6–311+G(d), aug-cc-PVDZ and the recently developed Z3PolX basis sets. Moreover, the first-order hyperpolarizability was calculated at the coupled cluster singles and doubles (CCSD/6–31+G(d)) level of theory. The analysis of the results of calculations for the investigated isomers indicates that there are important differences in their NLO activities. Additionally, it was shown that Z3PolX basis set works reasonable well for betaine dyes.

Theoretical investigation on the structure and thermodynamic properties of the 2,4-dinitroimidazole complex with methanol

The structure and thermodynamic properties of the 2, 4-dinitroimidazole complex with methanol were investigated using the B3LYP and MP2(full) methods with the 6-31++G(2d,p) and 6-311++G(3df,2p) basis sets. Four types of hydrogen bonds [N–H?O, C–H?O, O–H?O (nitro oxygen) and O–H?π] were found. The hydrogen-bonded complex having the highest binding energy had a N–H?O hydrogen bond. Analyses of natural bond orbital (NBO) and atoms-in-molecules (AIM) revealed the nature of the intermolecular hydrogen-binding interaction. The changes in thermodynamic properties from monomers to complexes with temperatures ranging from 200.0 to 800.0 K were investigated using the statistical thermodynamic method. Hydrogen-bonded complexes of 2,4-dinitroimidazole with methanol are fostered by low temperatures.

Quantum chemical investigation of the intra- and intermolecular proton transfer reactions and hydrogen bonding interactions in 4-amino-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione

The intramolecular thione-thiol tautomerism and intermolecular double proton transfer reaction of the hydrogen-bonded thione and thiol dimers in the title triazole compound were studied at the B3LYP level of theory using 6?311++G(d,p) basis function. The influence of the solvent on the single and double proton transfer reactions was examined in three solvents (chloroform, methanol and water) using the polarizable continuum model (PCM) approximation. The computational results show that the thione tautomer is the most stable isomer with a very high tautomeric energy barrier both in the gas phase and in solution phase, indicating a quite disfavored process. The solvent effect is found to be sizable with increasing polarity. In the double proton transfer reaction, the thione dimer is found to be more stable than thiol dimer both in the gas phase and in solution phase. The energetic and thermodynamic parameters of the double proton transfer process show that the double proton exchange from thione dimer to thiol dimer is thermodynamically unfavored. However, the exchange from thiol dimer to thione dimer for the gas phase and water phase seems to be feasible with a low barrier height and with a negative value in enthalpy and free energy changes. In addition, the hydrogen bonding interactions were analyzed in the gas phase regarding their geometries and energies. It is found that all complex formations are enthalpically favored, and the stability of the H-bonds comes in the order of S1—H2···N2 > N2—H2···S1 > N3—H3B···O1. Finally, non-linear optical properties were carried out at the same calculation level in the gas phase.

Improved hybrid optimization algorithm for 3D protein structure prediction

Diuron, a chlorine-substituted dimethyl herbicide, is widely used in agriculture. Though the degradation of diuron in water has been studied much with experiments, little is known about the detailed degradation mechanism from the molecular level. In this work, the degradation mechanisms for OH-induced reactions of diuron in water phase are investigated at the MPWB1K/6–311+G(3df,2p)//MPWB1K/6–31+G(d,p) level with polarizable continuum model (PCM) calculation. Three reaction types including H-atom abstraction, addition, and substitution are identified. For H-atom abstraction reactions, the calculation results show that the reaction abstracting H atom from the methyl group has the lowest energy barrier; the potential barrier of ortho- H (H1’) abstraction is higher than the meta- H abstraction, and the reason is possibly that part of the potential energy is to overcome the side chain torsion for the H1’ abstraction reaction. For addition pathways, the ortho- site (C (2) atom) is the most favorable site that OH may first attack; the potential barriers for OH additions to the ortho- sites (pathways R7 and R8) and the chloro-substituted para- site (R10) are lower than other sites, indicating the ortho- and para- sites are more favorable to be attacked, matching well with the -NHCO- group as an ortho-para directing group.

DFT studies of the conversion of four mesylate esters during reaction with ammonia

The energetics of the Menshutkin-like reaction between four mesylate derivatives and ammonia have been computed using B3LYP functional with the 6-31+G** basis set. Additionally, MPW1K/6-31+G** level calculations were carried out to estimate activation barrier heights in the gas phase. Solvent effect corrections were computed using PCM/B3LYP/6-31+G** level. The conversion of the reactant complexes into ion pairs is accompanied by a strong energy decrease in the gas phase and in all solvents. The ion pairs are stabilized with two strong hydrogen bonds in the gas phase. The bifurcation at C2 causes a significant activation barrier increase. Also, bifurcation at C5 leads to noticeable barrier height differentiation. Both B3LYP/6-31+G** and MPW1K/6-31+G** activation barriers suggest the reaction 2 (2a?+?NH₃) to be the fastest in the gas phase. The reaction 4 is the slowest one in all environments.

Synthesis of enantiomeric pureCis-dichloroplatinum(II) amino acid complexes

The reaction of potassium tetrachloroplatinate(II) with six representative sulfurcontaining amino acids, namely,d- andl-cysteine,d- andl-methionine and its methyl ester hydrochloride gives the corresponding enantiomerically purecis-dichloroplatinum(II) complexes. This represents the first reported series of well-characterized enantiomerically pure platinum(II) complexes for bothd- andl-amino acids. The spectroscopic properties, including IR,¹H-NMR, and¹³C NMR, of these complexes and their configuration are discussed.     

Electronic, ductile, phase transition and mechanical properties of Lu-monopnictides under high pressures

The structural, elastic and electronic properties of lutatium-pnictides (LuN, LuP, LuAs, LuSb, and LuBi) were analyzed by using full-potential linearized augmented plane wave within generalized gradient approximation in the stable rock-salt structure (B1 phase) with space group Fm-3m and high-pressure CsCl structure (B2 phase) with space group Pm-3m. Hubbard-U and spin-orbit coupling were included to predict correctly the semiconducting band gap of LuN. Under compression, these materials undergo first-order structural transitions from B1 to B2 phases at 241, 98, 56.82, 25.2 and 32.3 GPa, respectively. The computed elastic properties show that LuBi is ductile by nature. The electronic structure calculations show that LuN is semiconductor at ambient conditions with an indirect band gap of 1.55 eV while other Lu-pnictides are metallic. It was observed that LuN shows metallization at high pressures. The structural properties, viz, equilibrium lattice constant, bulk modulus and its pressure derivative, transition pressure, equation of state, volume collapse, band gap and elastic moduli, show good agreement with available data.

Perspectives on the reaction force constant

A synchronous, concerted chemical process is rigorously divided by the reaction force F(R), the negative gradient of V(R), into “reactant” and “product” regions which are dominated by structural changes and an intervening “transition” region which is electronically intensive. The reaction force constant κ(R), the second derivative of V(R), is negative throughout the transition region, not just at the nominal transition state, at which κ(R) has a minimum. This is consistent with experimental evidence that there is a transition region, not simply a specific point. We show graphically that significant nonsynchronicity in the process is associated with the development of a maximum of κ(R) in the transition region, which increases as the process becomes more nonsynchronous. (We speculate that for a nonconcerted process this maximum is actually positive.) Thus, κ(R) can serve as an indicator of the level of nonsynchronicity.

Stability and electronic properties of 3D covalent organic frameworks

Covalent organic frameworks (COFs) are a class of covalently linked crystalline nanoporous materials, versatile for nanoelectronic and storage applications. 3D COFs, in particular, have very large pores and low mass densities. Extensive theoretical studies of their energetic and mechanical stability, as well as their electronic properties, have been carried out for all known 3D COFs. COFs are energetically stable and their bulk modulus ranges from 3 to 20 GPa. Electronically, all COFs are semiconductors with band gaps corresponding to the HOMO–LUMO gaps of the building units.

Variation of the electronic dipole polarizability on the reaction path

The reaction force and the electronic flux, first proposed by Toro-Labbé et al. (J Phys Chem A 103:4398, 1999) have been expressed by the existing conceptual DFT apparatus. The critical points (extremes) of the chemical potential, global hardness and softness have been identified by means of the existing and computable energy derivatives: the Hellman-Feynman force, nuclear reactivity and nuclear stiffness. Specific role of atoms at the reaction center has been unveiled by indicating an alternative method of calculation of the reaction force and the reaction electronic flux. The electron dipole polarizability on the IRC has been analyzed for the model reaction HF + CO→HCOF. The electron polarizability determined on the IRC α _e (ξ) was found to be reasonably parallel to the global softness curve S(ξ). The softest state on the IRC (not TS) coincides with zero electronic flux.

A comparative DFT study on aquation and nucleobase binding of ruthenium (II) and osmium (II) arene complexes

The potential energy surfaces of the reactions of organometallic arene complexes of the type [(η ⁶-arene)M^II(pic)Cl] (where pic = 2-picolinic acid, M = Ru or Os) were examined by a DFT computational study. Among the seven density functional methods, hybrid exchange functional B3LYP outperforms the others to explain the aquation of the complexes. The reactions and binding energies of Ru^II and Os^II arene complexes with both 9EtG and 9EtA were studied to gain insight into the reactivity of these types of organometallic complexes with DNA. The obtained data rationalize experimental observation, contributing to partly understanding the potential biological and medical applications of organometallic complexes.