Computational comparison of the kinetic stabilities of diamino- and diamidocarbenes in the 1,2-H shift reaction

In this study, we performed several DFT, MP2, and BD(T) calculations on the 1,2-H shift reactions of two diaminocarbenes (1, 2) and a diamidocarbene (3) using the Gaussian 09 program. In Gaussian 09, the BD(T) method keyword requests a Brueckner doubles calculation including a perturbative triples contribution. Although N-heterocyclic carbenes (NHC) are typically known for their exceptional σ-donor abilities, recent studies have indicated that π-interactions also play a role in the bonding between NHCs and transition metals or BX₃ (X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br) (Nemcsok et al. Organomet 23:3640–3646, 2004, Esrafili. J Mol Model 18:2003–2011, 2012). In order to study the importance of π-interactions between carbenes and transition metals, Hobbs and co-workers (Hobbs et al. New J Chem 34:1295–1308, 2010) focused on the synthesis of NHCs with reduced-energy lowest unoccupied molecular orbitals. By introducing an oxalamide moiety into the heterocyclic backbone, they found the resulting carbene possessed higher electrophilicity than usual NHCs. According to our results, the N,N'-diamidocarbene should be more stable than the diaminocarbenes with respect to the 1,2-H shift reaction.

Prediction of thermodynamically reversible hydrogen storage reactions utilizing Ca–M(M = Li, Na, K)–B–H systems: a first-principles study

Calcium borohydride is a potential candidate for onboard hydrogen storage because it has a high gravimetric capacity (11.5 wt.%) and a high volumetric hydrogen content (～130 kg m^?3). Unfortunately, calcium borohydride suffers from the drawback of having very strongly bound hydrogen. In this study, Ca(BH₄)₂ was predicted to form a destabilized system when it was mixed with LiBH₄, NaBH₄, or KBH₄. The release of hydrogen from Ca(BH₄)₂ was predicted to proceed via two competing reaction pathways (leading to CaB₆ and CaH₂ or CaB₁₂H₁₂ and CaH₂) that were found to have almost equal free energies. Using a set of recently developed theoretical methods derived from first principles, we predicted five new hydrogen storage reactions that are among the most attractive of those presently known. These combine high gravimetric densities (>6.0 wt.% H₂) with have low enthalpies [approximately 35 kJ/(mol^?1 H₂)] and are thermodynamically reversible at low pressure within the target window for onboard storage that is actively being considered for hydrogen storage applications. Thus, the first-principles theoretical design of new materials for energy storage in future research appears to be possible.

Effects of trimethylaluminium and tetrakis(ethylmethylamino) hafnium in the early stages of the atomic-layer-deposition of aluminum oxide and hafnium oxide on hydroxylated GaN nanoclusters

We calculate the interactions of two atomic layer deposition (ALD) reactants, trimethylaluminium (TMA) and tetrakis(ethylmethylamino) hafnium (TEMAH) with the hydroxylated Ga-face of GaN clusters when aluminum oxide and hafnium oxide, respectively, are being deposited. The GaN clusters are suitable as testbeds for the actual Ga-face on practical GaN nanocrystals of importance not only in electronics but for several other applications in nanotechnology. We find that TMA spontaneously interacts with hydroxylated GaN; however it does not follow the atomic layer deposition reaction path unless there is an excess in potential energy introduced in the clusters at the beginning of the optimization, for instance, using larger bond lengths of various bonds in the initial structures. TEMAH also does not interact with hydroxylated GaN, unless there is an excess in potential energy. The formation of a Ga—N(CH₃)(CH₂CH₃) bond during the ALD of HfO₂ using TEMAH as the reactant without breaking the Hf—N bond could be the key part of the mechanism behind the formation of an interface layer at the HfO₂/GaN interface.

Electron density reactivity indexes of the tautomeric/ionization forms of thiamin diphosphate

The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6–31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reactivity. The results allow to conclude that the highly conserved glutamic residue does not protonate the N1′ atom of the pyrimidyl ring, but it participates in a strong hydrogen bonding, stabilizing the eventual negative charge on the nitrogen, in all forms involved in the ylide generation. This condition provides the necessary reactivity on key atoms, N4′ and C2, to carry out the formation of the ylide required to initiate the catalytic cycle of ThDP- dependent enzymes. This study represents a new approach for the ylide formation in ThDP catalysis.

A molecular dynamics study on sI hydrogen hydrate

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

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.

Electric field effect on the zigzag (6,0) single-wall BC2N nanotube for use in nano-electronic circuits

We have analyzed the effect of external electric field on the zigzag (6,0) single-wall BC₂N nanotube using density functional theory calculations. Analysis of the structural parameters indicates that the nanotube is resistant against the external electric field strengths. Analysis of the electronic structure of the nanotube indicates that the applied parallel electric field strengths have a much stronger interaction with the nanotube with respect to the transverse electric field strengths and the nanotube is easier to modulate by the applied parallel electric field. Our results show that the properties of the nanotube can be controlled by the proper external electric field for use in nano-electronic circuits.

Theoretical investigation into optical and electronic properties of 1,8-naphthalimide derivatives

A series of 1,8-naphthalimide derivatives has been designed to explore their optical, electronic, and charge transport properties as charge transport and/or luminescent materials for organic light-emitting diodes (OLEDs). The frontier molecular orbitals (FMOs) analysis have shown that the vertical electronic transitions of absorption and emission are characterized as intramolecular charge transfer (ICT) for electron-donating and aromatic groups substituted derivatives. However, the ICT character of the electron-withdrawing substituted derivatives is not significant. The calculated results show that their optical and electronic properties are affected by the substituent groups in 4-position of 1,8-naphthalimide. Our results suggest that 1,8-naphthalimide derivatives with electron-donating ?OCH₃ and ?N(CH₃)₂ (1 and 2), electron-withdrawing ?CN and?COCH₃ (3 and 4), 2-(thiophen-2-yl)thiophene (5), 2,3-dihydrothieno[3,4-b][1, 4]dioxine (6), 2-phenyl-1,3,4-oxadiazole (7), and benzo[c][1,2,5]thiadiazole (8) fragments are expected to be promising candidates for luminescent materials for OLEDs, particularly for 5 and 7. In addition, 3 and 7 can be used as promising hole transport materials for OLEDs. This study should be helpful in further theoretical investigations on such kind of systems and also to the experimental study for charge transport and/or luminescent materials for OLEDs.

Theoretical study of the triangular bonding complex formed by carbon tetrabromide, a halide, and a solvent molecule in the gas phase

MP2(full)/aug-cc-pVDZ(-PP) computations predict that new triangular bonding complexes (where X^? is a halide and H–C refers to a protic solvent molecule) consist of one halogen bond and two hydrogen bonds in the gas phase. Carbon tetrabromide acts as the donor in the halogen bond, while it acts as an acceptor in the hydrogen bond. The halide (which commonly acts as an acceptor) can interact with both carbon tetrabromide and solvent molecule (CH₃CN, CH₂Cl₂, CHCl₃) to form a halogen bond and a hydrogen bond, respectively. The strength of the halogen bond obeys the order CBr₄???Cl^? > CBr₄???Br^? > CBr₄???I^?. For the hydrogen bonds formed between various halides and the same solvent molecule, the strength of the hydrogen bond obeys the order C-H???Cl^? > C-H???Br^? > C-H???I^?. For the hydrogen bonds formed between the same halide and various solvent molecules, the interaction strength is proportional to the acidity of the hydrogen in the solvent molecule. The diminutive effect is present between the hydrogen bonds and the halogen bond in chlorine and bromine triangular bonding complexes. Complexes containing iodide ion show weak cooperative effects.

Computationally designed prodrugs of statins based on Kirby’s enzyme model

DFT calculations at B3LYP/6-31G(d,p) for intramolecular proton transfer in Kirby’s enzyme models 1–7 demonstrated that the reaction rate is dependent on the distance between the two reacting centers, r_GM, and the hydrogen bonding angle, α, and the rate of the reaction is linearly correlated with r_GM and α. Based on these calculation results three simvastatin prodrugs were designed with the potential to provide simvastatin with higher bioavailability. For example, based on the calculated log EM for the three proposed prodrugs, the interconversion of simvastatin prodrug ProD 3 to simvastatin is predicted to be about 10 times faster than that of either simvastatin prodrug ProD 1 or simvastatin ProD 2. Hence, the rate by which the prodrug releases the statin drug can be determined according to the structural features of the promoiety (Kirby’s enzyme model).

Excited-state relaxation paths of oxo/hydroxy and N9H/N7H tautomers of guanine: a CC2 theoretical study

We performed a theoretical investigation, at the CC2/aug-cc-pVDZ level, of the ring-deformation mechanisms of four guanine tautomers (oxo, hydroxy, N9H, and N7H). The study showed that the optimized conical intersections S₀/S₁ are accessible through the ¹ππ* excited states of tautomers. The optimized conical intersections S₀/S₁, which show deformation at the pyrimidine ring, have high energies. This means that the relaxations of the ¹ππ* excited states via internal conversion are disfavored. For two tautomers we found crossing points ¹ππ*/¹πσ* of the excited-state reaction paths, revealing the possibility of a population of the ¹πσ* excited state by the ¹ππ* excited state.

Theoretical study on the binding mechanism between N6-methyladenine and natural DNA bases

N6-methyladenine (m⁶A) is a rare base naturally occurring in DNA. It is different from the base adenine due to its N-CH₃. Therefore, the base not only pairs with thymine, but also with other DNA bases (cytosine, adenine and guanine). In this work, Møller-Plesset second-order (MP2) method has been used to investigate the binding mechanism between m⁶A and natural DNA bases in gas phase and in aqueous solution. The results show that N-CH₃ changed the way of N6-methyladenine binding to natural DNA bases. The binding style significantly influences the stability of base pairs. The trans-m⁶A:G and trans-m⁶A:C conformers are the most stable among all the base pairs. The existence of solvent can remarkably reduce the stability of the base pairs, and the DNA bases prefer pairing with trans-m⁶A to cis-m⁶A. Besides, the properties of these hydrogen bonds have been analyzed by atom in molecules (AIM) theory, natural bond orbital (NBO) analysis and Wiberg bond indexes (WBI). In addition, pairing with m⁶A decreases the binding energies compared to the normal Watson-Crick base pairs, it may explain the instability of the N6 site methylated DNA in theory.

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.

A new interaction mechanism of LiNH2 with MgH2: magnesium bond

Quantum chemical calculations were performed for LiNH₂–HMgX (X?=?H, F, Cl, Br, CH₃, OH, and NH₂) complexes to propose a new interaction mechanism between them. This theoretical survey showed that the complexes are stabilized through the combinative interaction of magnesium and lithium bonds. The binding energies are in the range of 63.2–66.5 kcal mol^?1, i.e., much larger than that of the lithium bond. Upon complexation, both Mg–H and Li–N bonds are lengthened. Substituents increase Mg-H bond elongation and at the same time decrease Li-N bond elongation. These cyclic complexes were characterized with the presence of a ring critical point and natural population analysis charges.

Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3′-O, 5′-S) thymidine phosphodiester derivatives

Hydrolysis of nucleic acids is of fundamental importance in biological sciences. Kinetic and theoretical studies on different substrates wherein the phosphodiester bond combined with alkyl or aryl groups and sugar moiety have been the focus of attention in recent literature. The present work focuses on understanding the mechanism and energetics of alkali metal (Li, Na, and K) catalyzed hydrolysis of phosphodiester bond in modeled substrates including Thymidylyl (3′-O, 5′-S) thymidine phosphodiester (Tp-ST) (1), 3′-Thymidylyl (1-trifluoroethyl) phosphodiester (Tp-OCH₂CF₃) (2), 3′-Thymidylyl (o-cholorophenyl) phosphodiester (Tp-OPh(o-Cl)) (3) and 3′-Thymidylyl(p-nitrophenyl) phosphodiester (Tp-OPh(p-NO₂)) (4) employing density functional theory. Theoretical calculations reveal that the reaction follows a single-step (A_ND_N) mechanism where nucleophile attack and leaving group departure take place simultaneously. Activation barrier for potassium catalyzed Tp-ST hydrolysis (12.0 kcal mol^?1) has been nearly twice as large compared to that for hydrolysis incorporating lithium or sodium. Effect of solvent (water) on activation energies has further been analyzed by adding a water molecule to each metal ion of the substrate. It has been shown that activation barrier of phosphodiester hydrolysis correlates well with basicity of leaving group.

Relativistic theoretical studies on hydrogen bonds and the electronic structure of aqueous solvated bis(uranyl) complex: an insight into explicit and/or implicit solvent effects

To understand the chemical behavior of uranyl complexes in water, a bis-uranyl [(phen)(UO₂)(μ₂–F)(F)]₂ (A; phen?=?phenanthroline, μ₂?=?doubly bridged) and its hydrated form A?·?(H₂O)_n (n?=?2, 4 and 6) were examined using scalar relativistic density functional theory. The addition of water caused the phen ligands to deviate slightly from the U₂(μ₂–F)₂ plane, and red-shifts the U–F-terminal and U?=?O stretching vibrations. Four types of hydrogen bonds are present in the optimized hydrated A?·?(H₂O)_n complexes; their energies were calculated to fall within the range 4.37–6.77 kcal mol^-1, comparable to the typical values of 5.0 kcal mol^-1 reported for hydrogen bonds. An aqueous environment simulated by explicit and/or implicit models lowers and re-arranges the orbitals of the bis-uranyl complex.

Theoretical study of hydrogen bonding interactions on MDI-based polyurethane

Hydrogen bonding among hard–hard segments and hard–soft segments in 4,4′-diphenylmethane diisocyanate (MDI)-based polyurethane was investigated theoretically by density functional theory (DFT). Both B3LYP/6-31G* and B3PW91/6-31G* methods gave good structures, reasonable Mulliken charges, binding energies, dipole moments, and good infrared (IR) spectra trends in predicting hydrogen bonding. Bond distances R(N–H?O), which were in the range of 3.005–3.028 Å for the carbonyl bonded hydrogen-bond, and 3.074–3.075 Å for the ester bonded hydrogen-bond, are in reasonable agreement with experimental values. Most of the carbonyl oxygen in polyurethane exists in a hydrogen-bonded form. Complex (c), with two carbonyl hydrogen bonds, features the largest dipole moment, while complex (d) with two ester hydrogen bonds, possesses the smallest dipole moment, i.e., lower than that of the isolated monomer, which may be due to the symmetry of the two monomers. These results confirm that the DFT method is a good tool with which to study weak interactions, and indicate that hydrogen bonds are indeed formed between carbonyl and N-H, or ester and N-H, with the former being stronger.

Ruthenium hydride-catalyzed regioselective addition of benzaldehyde to dienes leading to β,γ-unsaturated ketones: a DFT study

Density functional theory (DFT) was used to investigate the ruthenium hydride-catalyzed regioselective addition reactions of benzaldehyde to isoprene leading to the branched β,γ-unsaturated ketone. All intermediates and the transition states were optimized completely at the B3LYP/6-31?G(d,p) level (LANL2DZ(f) for Ru, LANL2DZ(d) for P and Cl). Calculated results indicated that three catalysts RuHCl(CO)(PMe₃)₃ (1), RuH₂(CO)(PMe₃)₃ (2), and RuHCl(PMe₃)₃ (3) exhibited different catalysis, and the first was the most excellent. The most favorable reaction pathway included the coordination of 1 to the less substituted olefin of isoprene, a hydrogen transfer reaction from ruthenium to the carbon atom C1, the complexation of benzaldehyde to ruthenium, the carbonyl addition, and the hydride elimination reaction. The carbonyl addition was the rate-determining step. The dominant product was the branched β,γ-unsaturated ketone. Furthermore, the presence of one toluene molecule lowered the activation free energy of the transition state of the carbonyl addition by hydrogen bonds between the protons of toluene and the chlorine, carbonyl oxygen of the ruthenium complex. On the whole, the solvent effect decreased the free energies of the species.

Theoretical study of the solvatochromism of a donor-acceptor bithiophene

The solvation and the solvatochromic behavior of the 5-(methylthio)-5′-nitro-2,2′-bithiophene 1 in diethyl ether, dichloromethane, acetonitrile, methanol and formamide was theoretically investigated with an iterative molecular and quantum mechanics (QM/MM) approach. Calculated longest-wavelength solvatochromic absorption band of 1, obtained as averages of statistically uncorrelated configurations, including the solute and explicit solvent molecules of the first and second solvation layer, were in excellent agreement with the experimental results.