Theoretical study of structural patterns in CH<Subscript>2</Subscript>OP<Subscript>2</Subscript> isomers

DFT calculations have been performed on the derivatives of formula CH₂OP₂ to determine their total energy, the relative energy between the isomers and their geometry. Among compounds with a P-C-P linkage, the most stable one is the 2-hydroxy-1,2-diphosphirene II.1, a three-membered heterocycle with a P=C unsaturation. The phosphavinylidene(oxo)phosphorane HP=C=P(O)H IV.5 (which has the same skeleton as the experimentally obtained Mes*P=C=P(O)Mes*) lies 36.30 kcal mol^-1 above it. The least stable compounds are carbenes; the singlet carbenes are more stable than the triplet ones.     

Influence of cis-[PtCl<Subscript>2</Subscript>(Me<Subscript>2</Subscript>SO)<Subscript>2</Subscript>] on thermal denaturation of albumin

The interaction of cis-[PtCl₂(Me₂SO)₂] with human serum albumin (HSA) and the sensitivity of the complex to heat denaturation as dependent on the duration of incubation have been studied by UV absorption and fluorescence spectroscopy. Optimal conditions for cis-[PtCl₂(Me₂SO)₂] binding to HSA have been determined. The results are compared with the data for the HSA-cisplatin complex. It has been found that binding of HSA with cis-[PtCl₂(Me₂SO)₂] does not result in significant structural changes of the protein.     

Electronic structure and bonding of the dinuclear metal M<Subscript>2</Subscript>(CO)<Subscript>10</Subscript> decacarbonyls: applications of natural orbitals for chemical valence

The nature of the chemical metal–metal bond in M₂(CO)₁₀ (M?=?Mn, Re, Tc) dinuclear decacarbonyls complexes was investigated for the first time using the natural orbital chemical valence (NOCV) approach combined with the extended transition state (ETS) for energy decomposition analysis (EDA). The optimized geometries carried out at different levels of theory BP86, BLYP, BLYPD and BP86D, showed that the latter method, i.e., BP86D, led to the best agreement with X-ray experimental measurements. The BP86D/TZP results revealed that the computed covalent contribution to the metal–metal bond are 60.5%, 54.1% and 52.0% for Mn–Mn, Re–Re and Tc–Tc, respectively. The computed total interaction energies resulting from attractive terms (ΔE _orb and ΔE _eles), correspond well to experimental predictions, based on bond lengths and energy interaction analysis for the studied complexes.     

DFT study of CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O co-adsorption on carbon models of coal surface

The moisture content of coal affects the adsorption capacity of CO₂ on the coal surface. Since the hydrogen bonds are formed between H₂O and oxygen functional group, the H₂O cluster more easily adsorbs on the coal micropore than CO₂ molecule. The coal micropores are occupied by H₂O molecules that cannot provide extra space for CO₂ adsorption, which may leads to the reduction of CO₂ adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO₂ and adsorbed H₂O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H₂O to CO₂ adsorption. This study reports some typical coal-H₂O···CO₂ complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H₂O molecule can more stably adsorb on the aromatic ring surface than CO₂ molecule, and the absolute values of local ESP maximum and minimum of H₂O cluster are greater than CO₂. AIM analysis shows a detailed interaction path and strength between atoms in CO₂ and H₂O, and RDG analysis shows that the interactions among CO₂, H₂O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO₂ and H₂O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H₂O can promote CO₂ adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO₂ adsorption capacity, the attractive interaction of adsorbed H₂O to CO₂ makes little contribution.     

Synthesis of Protein-Inorganic Nanohybrids with Improved Catalytic Properties Using Co<Subscript>3</Subscript>(PO<Subscript>4</Subscript>)<Subscript>2</Subscript>

In the present study, a method for easy and rapid synthesis of lipase nanohybrids was evaluated using cobalt chloride as an encapsulating agent. The synthesized nanohybrids exhibited higher activity (181%) compared to free lipase and improved catalytic properties at higher temperature and in harsh conditions. The nanohybrids retained 84% of their residual activity at 25 °C after 10 days. In addition, these nanohybrids also exhibited high storage stability and reusability. Collectively, the synthesis of carrier-free immobilized biocatalysts was performed rapidly within 24 h at 4 °C. Their high reusability and catalytic activities highlight the broad applicability of this method for catalysis in organic and aqueous media.     

A DFT study of addition reaction between fragment ion (CH<Subscript>2</Subscript>) units and fullerene (C<Subscript>60</Subscript>) molecule

The theoretical study of the interaction between CH₂ and fullerene (C₆₀) suggests the existence of an addition reaction mechanism; this feature is studied by applying an analysis of electronic properties. Several different effects are evident in this interaction as a consequence of the particular electronic transfer which occurs during the procedure. The addition or insertion of the methylene group results in a process, where the inclusion of CH₂ into a fullerene bond produces the formation of several geometric deformations. A simulation of these procedures was carried out, taking advantage of the dynamic semi-classical Born-Oppenheimer approximation. Dynamic aspects were analyzed at different speeds, for the interaction between the CH₂ group and the two bonds: CC (6, 6) and CC (6, 5) respectively on the fullerene (C₆₀) rings. All calculations which involved electrons employed DFT as well as exchange and functional correlation. The results indicate a tendency for the CH₂ fragment to attack the CC (6, 5) bond.     

d(A)<Subscript>3</Subscript>d(T)<Subscript>3</Subscript> and d(G)<Subscript>3</Subscript>d(C)<Subscript>3</Subscript> B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics

We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)₃·d(T)₃ and d(G)₃·d(C)₃ nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra—molecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)₃d(T)₃ and d(G)₃d(C)₃ duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.     

Theoretical study of the reaction mechanism of CH<Subscript>3</Subscript>NO<Subscript>2</Subscript> with NO<Subscript>2</Subscript>, NO and CO: the bimolecular reactions that cannot be ignored

The intriguing decompositions of nitro-containing explosives have been attracting interest. While theoretical investigations have long been concentrated mainly on unimolecular decompositions, bimolecular reactions have received little theoretical attention. In this paper, we investigate theoretically the bimolecular reactions between nitromethane (CH₃NO₂)—the simplest nitro-containing explosive—and its decomposition products, such as NO₂, NO and CO, that are abundant during the decomposition process of CH₃NO₂. The structures and potential energy surface (PES) were explored at B3LYP/6-31G(d), B3P86/6-31G(d) and MP2/6-311?+?G(d,p) levels, and energies were refined using CCSD(T)/cc-pVTZ methods. Quantum chemistry calculations revealed that the title reactions possess small barriers that can be comparable to, or smaller than, that of the initial decomposition reactions of CH₃NO₂. Considering that their reactants are abundant in the decomposition process of CH₃NO₂, we consider bimolecular reactions also to be of great importance, and worthy of further investigation. Moreover, our calculations show that NO₂ can be oxidized by CH₃NO₂ to NO₃ radical, which confirms the conclusion reached formerly by Irikura and Johnson [(2006) J Phys Chem A 110:13974–13978] that NO₃ radical can be formed during the decomposition of nitramine explosives.     

Theoretical study of the novel sandwich compound [Au<Subscript>3</Subscript>Cl<Subscript>3</Subscript>Tr<Subscript>2</Subscript>]<Superscript>2+</Superscript>

A theoretical study of a sandwich compound with a metal monolayer sheet between two aromatic ligands is presented. A full geometry optimization of the [Au₃Cl₃Tr₂]²⁺ (1) compound, which is a triangular gold(I) monolayer sheet capped by chlorines and bounded to two cycloheptatrienyl (Tr) ligands was carried out using perturbation theory at the MP2 computational level and DFT. Compound (1) is in agreement with the 18–electron rule, the bonding nature in the complex may be interpreted from the donation interaction coming from the Tr rings to the Au array, and from the back-donation from the latter to the former. NICS calculations show a strong aromatic character in the gold monolayer sheet and Tr ligands; calculations done with HOMA, also report the same aromatic behavior on the cycloheptatrienyl fragments giving us an insight on the stability of (1). The Au –Au bond lengths indicate that an intramolecular aurophilic interaction among the Au(I) cations plays an important role in the bonding of the central metal sheet. Figure (a) Ground state geometry of complex 1; (b) Top view of compound 1 and Wiberg bond orders computed with the MP2/B1 computational method; (c) Lateral view of compound 1 and NICS values calculated with the MP2/B1 method; the values in parenthesis were obtained at the VWN/TZP level     

Biological activity and binding properties of [Ru(II)(dcbpy)<Subscript>2</Subscript>Cl<Subscript>2</Subscript>] complex to bovine serum albumin,phospholipase A<Subscript>2</Subscript> and glutathione

Ruthenium compounds are highly regarded as metallo-drug candidates. Many studies have focused their attention on the interaction between ruthenium complexes with their possible biological targets. The interaction of ruthenium complexes with transport proteins, enzymes and peptides is of great importance for understanding their biodistribution and mechanism of action, therefore, the development of an anti-cancer therapy involving ruthenium complexes has recently shifted from DNA targeting towards protein targeting. With the aim of gaining insight into possible interactions between ruthenium complexes with biologically relevant proteins, we have studied the interaction of cis-dichlorobis(2,2′-bipyridyl-4,4′-dicarboxylic acid)ruthenium(II) complex [Ru(II)(dcbpy)₂Cl₂], which previously showed good potency in photo-dynamic chemotherapy, with bovine serum albumin (BSA), phospholipase A₂ (PLA₂) and glutathione (GSH). Binding constants and possible number of binding sites to mentioned proteins and peptide are investigated by ultraviolet–visible spectroscopy and Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI TOF MS). The complex binding affinities were in the following order: PLA₂ > BSA > GSH. Moreover, genotoxic profile of the complex, tested on peripheral blood lymphocytes as a model system, was also promising.     

DFT study of benzyl alcohol/TiO<Subscript>2</Subscript> interfacial surface complex: reaction pathway and mechanism of visible light absorption

We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO₂ and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO₂ surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H₂O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO₂ surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO₂ surface.

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Graphical Abstract The chemisorption of benzyl alcohol on TiO₂ surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light

     

The influence of Sc doping on structural,electronic and optical properties of Be<Subscript>12</Subscript>O<Subscript>12</Subscript>, Mg<Subscript>12</Subscript>O<Subscript>12</Subscript> and Ca<Subscript>12</Subscript>O<Subscript>12</Subscript> nanocages: a DFT study

Density functional theory (DFT) calculations were used to study the effect of scandium doping on the structural, energetic, electronic, linear and nonlinear optical (NLO) properties of Be₁₂O₁₂, Mg₁₂O₁₂ and Ca₁₂O₁₂ nanoclusters. Scandium (Sc) doping on nanoclusters leads to narrowing of their E _g, which enhances their conductance greatly. Also, the polarizability (α) and first hyperpolarizability (β₀) of nanoclusters were dramatically increased as Be, Mg or Ca atoms are substituted with a Sc atom. Among all clusters, α and β₀ values for Sc-doped Ca₁₂O₁₂ were the largest. Consequently, the effect of the doping atom, as well as of cluster size, on electronic and optical properties was explored. Time dependent (TD)-DFT calculations were also carried out to confirm the β₀ values; the results show that the higher value of first hyperpolarizability belongs to Sc-doped Ca₁₂O₁₂, which has the smallest transition energy (ΔEgn). The results obtained show that these clusters can be candidates for using in electronic devices and NLO materials in industry.     

TCNE-modified graphene as an adsorbent for N<Subscript>2</Subscript>O molecule: a DFT study

Adsorption behavior of nitrous oxide (N₂O) on pristine graphene (PG) and tetracyanoethylene (TCNE) modified PG surfaces is investigated using density functional theory. A number of initial adsorbate geometries are considered on both surfaces and the most stable ones are chosen upon calculation of the adsorption energies (E_ads). N₂O is found to adsorb in a weakly exoergic process (E_ads?～??3.18 kJ mol^?1) at the equilibrium distance of 3.52 Å on the PG surface. N₂O adsorption can be greatly enhanced with the presence of a TCNE molecule (E_ads?=??87.00 kJ mol^?1). Mulliken charge analysis confirms that adsorption of N₂O is not accompanied by distinct charge transfer from the surfaces to the molecule (? 0.001 │e│ for each case). Moreover, on the basis of calculated changes in the HOMO/LUMO energy gap, it is found that electronic properties of PG and TCNE modified PG are not sensitive toward adsorption of N₂O, indicating that both surfaces are not good enough to introduce as an N₂O detector. However, the considerable amount of E_ads in TCNE modified PG can be a guide to the design of graphene-based adsorbents for N₂O capture.     

Long chain fatty acyl-CoA modulation of H<Subscript>2</Subscript>O<Subscript>2</Subscript> release at mitochondrial complex I

Complex I is responsible for most of the mitochondrial H₂O₂ release, low during the oxidation of the NAD linked substrates and high during succinate oxidation, via reverse electron flow. This H₂O₂ production appear physiological since it occurs at submillimolar concentrations of succinate also in the presence of NAD substrates in heart (present work) and rat brain mitochondria (Zoccarato et al., Biochem J, 406:125–129, 2007). Long chain fatty acyl-CoAs, but not fatty acids, act as strong inhibitors of succinate dependent H₂O₂ release. The inhibitory effect of acyl-CoAs is independent of their oxidation, being relieved by carnitine and unaffected or potentiated by malonyl-CoA. The inhibition appears to depend on the unbound form since the acyl-CoA effect decreases at BSA concentrations higher than 2 mg/ml; it is not dependent on ΔpH or Δp and could depend on the inhibition of reverse electron transfer at complex I, since palmitoyl-CoA inhibits the succinate dependent NAD(P) or acetoacetate reduction.     

An effective approach for generating a three-Cys<Subscript>2</Subscript>His<Subscript>2</Subscript> zinc-finger-DNA complex model by docking

Background  

Determination of protein-DNA complex structures with both NMR and X-ray crystallography remains challenging in many cases. High Ambiguity-Driven DOCKing (HADDOCK) is an information-driven docking program that has been used to successfully model many protein-DNA complexes. However, a protein-DNA complex model whereby the protein wraps around DNA has not been reported. Defining the ambiguous interaction restraints for the classical three-Cys₂His₂ zinc-finger proteins that wrap around DNA is critical because of the complicated binding geometry. In this study, we generated a Zif268-DNA complex model using three different sets of ambiguous interaction restraints (AIRs) to study the effect of the geometric distribution on the docking and used this approach to generate a newly reported Sp1-DNA complex model.     

Bonding,aromaticity, and planar tetracoordinated carbon in Si<Subscript>2</Subscript>CH<Subscript>2</Subscript> and Ge<Subscript>2</Subscript>CH<Subscript>2</Subscript>

Natural bond orbital (NBO) analyses and dissected nucleus-independent chemical shifts (NICS _{π z z} ) were computed to evaluate the bonding (bond type, electron occupation, hybridization) and aromatic character of the three lowest-lying Si₂CH₂ (1-Si, 2-Si, 3-Si) and Ge₂CH₂ (1-Ge, 2-Ge, 3-Ge) isomers. While their carbon C₃H₂ analogs favor classical alkene, allene, and alkyne type bonding, these Si and Ge derivatives are more polarizable and can favor “highly electron delocalized”? and “non-classical”? structures. The lowest energy Si ₂CH₂ and Ge ₂CH₂ isomers, 1-Si and 1-Ge, exhibit two sets of 3–center 2–electron (3c-2e) bonding; a π-3c-2e bond involving the heavy atoms (C–Si–Si and C–Ge–Ge), and a σ-3c-2e bond (Si–H–Si, Ge–H–Ge). Both 3-Si and 3-Ge exhibit π and σ-3c-2e bonding involving a planar tetracoordinated carbon (ptC) center. Despite their highly electron delocalized nature, all of the Si₂CH₂ and Ge₂CH₂ isomers considered display only modest two π electron aromatic character (NICS(0) _{π z z} =--6.2 to –8.9 ppm, computed at the heavy atom ring center) compared to the cyclic-C ₃H₂ (–13.3 ppm).

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Graphical Abstract The three lowest Si2CH2 and Ge2CH2 isomers.

     

Molecular properties of metal difluorides and their interactions with CO<Subscript>2</Subscript> and H<Subscript>2</Subscript>O molecules: a DFT investigation

A computational study of metal difluorides (MF₂; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca–F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn–Teller effect in nonlinear MF₂ molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal. The interactions of CO₂ with ScF₂ (Scc3 geometry) and TiF₂ (Tic2 geometry) caused CO₂ to shift from its usual linear geometry to a bent geometry (η²(C=O) binding mode), while it retained its linear geometry (η¹(O) binding mode) when it interacted with the other metal difluorides. Energy decomposition analysis showed that, among the various geometries considered, the Scc3 and Tic2 geometries possessed the highest interaction energies and orbital interaction energies. Heavier transition metal difluorides showed stronger affinities for H₂O, whereas the lighter transition metal (Sc and Ti) difluorides preferred CO₂. Overall, the results of this study suggest that fluorides of lighter transition metals with partially filled d orbitals (e.g., Sc and Ti) could be used for CO₂ capture under moist conditions.

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Graphical abstract Interaction of metal difluorides with carbon dioxide and water

     

The encapsulated lithium effect on the first hyperpolarizability of C<Subscript>60</Subscript>Cl<Subscript>2</Subscript> and C<Subscript>60</Subscript>F<Subscript>2</Subscript>

In this paper, we report a study on the structure and first hyperpolarizability of C₆₀Cl₂ and C₆₀F₂. The calculation results show that the first hyperpolarizabilities of C₆₀Cl₂ and C₆₀F₂ were 172 au and 249 au, respectively. Compared with the fullerenes, the first hyperpolarizability of C₆₀Cl₂ increased from 0 au to 172 au, while the first hyperpolarizability of C₆₀F₂ increased from 0 au to 249 au. In order to further increase the first hyperpolarizability of C₆₀Cl₂ and C₆₀F₂, Li@C₆₀Cl₂ and Li@C₆₀F₂ were obtained by introducing a lithium atom to C₆₀Cl₂ and C₆₀F₂. The first hyperpolarizabilities of Li@C₆₀Cl₂ and Li@C₆₀F₂ were 2589 au and 985 au, representing a 15-fold and 3.9-fold increase, respectively, over those of C₆₀Cl₂ and C₆₀F₂. The transition energies of four molecules (C₆₀Cl₂, Li@C₆₀Cl₂, C₆₀F₂, Li@C₆₀F₂) were calculated, and were found to be 0.17866 au, 0.05229 au, 0.18385 au, and 0.05212 au, respectively. A two-level model explains why the first hyperpolarizability increases for Li@C₆₀Cl₂ and Li@C₆₀F₂.     

Distribution of calcium-independent phospholipase A<Subscript>2</Subscript> (iPLA<Subscript>2</Subscript>) in monkey brain

The present study was carried out to elucidate the distribution of calcium-independent phospholipase A₂ (iPLA₂) in the normal monkey brain. iPLA₂ immunoreactivity was observed in structures derived from the telencephalon, including the cerebral neocortex, amygdala, hippocampus, caudate nucleus, putamen, and nucleus accumbens, whereas structures derived from the diencephalon, including the thalamus, hypothalamus and globus pallidus were lightly labeled. The midbrain, vestibular, trigeminal and inferior olivary nuclei, and the cerebellar cortex were densely labeled. Immunoreactivity was observed on the nuclear envelope of neurons, and dendrites and axon terminals at electron microscopy. Western blot analysis showed higher levels of iPLA₂ protein in the cytosolic, than the nuclear fraction, but little or no protein in the membrane fraction. Similarly, subcellular fractionation studies of iPLA₂ activity in rat brain cortical cell cultures showed greater enzymatic activity in the cytosolic, than the nuclear fraction, and the least activity in non-nuclear membranes. The association of iPLA₂ with the nuclear envelope suggests a role of the enzyme in nuclear signaling, such as during neuronal proliferation and differentiation or death. In addition, the localization of iPLA₂ in dendrites and axon terminals suggests a role of the enzyme in neuronal signaling.     

Interaction of a Ti-doped semi-fullerene (TiC<Subscript>30</Subscript>) with molecules of CO and CO<Subscript>2</Subscript>

Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C₆₀ fullerene (i.e., C₃₀), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titanium atom on C₃₀ occurs in the concave surface of the molecule. Afterward, we investigated the interaction of the system C₃₀-titanium with carbon monoxide and carbon dioxide molecules, respectively. We found that each of these molecules is chemisorbed, with no dissociation. The value of the adsorption energy for the carbon monoxide molecule varies from ?0.897 to ?1.673 eV, and for the carbon dioxide molecule, it is between ?1.065 and ?1.274 eV. These values depend on the initial orientation of these molecules with respect to TiC₃₀.

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Graphical Abstract The TiC₃₀ system chemisorbs CO or CO₂?with no dissociation at atmospheric pressure and 300K