Initio Study Research Articles

Ab initio and DFT benchmark study for the calculations of isotopic shifts of fundamental frequencies for 2,3-dihydropyran

Ab initio and DFT benchmark study for the calculations of isotopic shifts of fundamental frequencies for 2,3-dihydropyran

Ab initio adiabatic study of the AgH system

In the framework of the Born–Oppenheimer (BO) method, we illustrate our ab-initio spectroscopic study of the of silver hydride molecule. The calculation of 48 electrons for this system is very difficult, so we have been employed a pseudo-potential (P.P) to reduce the big number of electrons to two electrons of valence, which is proposed by Barthelat and Durant. This allowed us to make a configuration interaction (CI). The potential energy curves (PECs) and the spectroscopic constants of AgH have been investigated for Σ+, Π and Δ symmetries. We have been determined the permanent and transition dipole moments (PDM and TDM), the vibrational energies levels and their spacing. We compared our results with the available experimental and theoretical results in the literature. We found a good accordance with the experimental and theoretical data that builds a validation of the choice of our approach.

Ab initio structure determination and morphology study of La1.26 Zr0.25 Na2.5 N0.24 O2.54 triclinic structure from powder x-ray diffraction data.

This paper deals with the ab initio structure determination of La1.26 N0.24 Na2.5 O2.54 Zr0.25 triclinic structure having triclinic crystal system via powder X-ray data using the Rietveld refinement method, and with physical properties characterization of a related solid solution at the room temperature structure of three compounds belonging to the Aurivillius family La1.26 N0.24 Na2.5 O2.54 Zr0.25 has been analyzed. La1.26 N0.24 Na2.5 O2.54 Zr0.25 crystallizes in a triclinic crystal system with P-1 space group. The starting material was Na2CO3,Zr(NO3)4 La2O3 for the Zr,La and Na analogues was derived from ab initio methods and refined using the Rietveld refinement method using JANA software package and visualization by Diamond computer program. The cations Na and La are disordered over the Zr sites while the La cation is found exclusively in the layers. The cell parameters are a=4.1040 Å b=9.9102 Å c=17.6117 Å α=98.4299° β=93.4378° γ=92.2041°.The morphology and electrical properties are carried out of cited oxide.

Tube-shaped molecular structures built from acylphloroglucinols: an ab initio and DFT study

Molecular structures containing a cavity encounter a variety of applications, from hosts to ions or to smaller molecules to building units for nanomaterials. Previous computational studies of bowl-shaped structures built from acylphloroglucinol (ACPL) units had shown that ACPLs can form the deepest cavities among hydroxybenzenes. The current work considers tube-shaped structures built from ACPL units. To ensure that the two rims have equal size, the orientations of the even-number units are alternated, so that each rim contains alternating RCO and OH-only groups from neighbouring units. Tubes with 4 and 6 units and different R chains have been calculated at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels. In each rim, the space between two consecutive RCO groups contains three consecutive intramolecular hydrogen bonds (IHBs). The computable properties of the calculated tubes are analysed in detail, with particular attention to the tubes’ geometric features (including the size of the hollow inner part) and to the characteristics and roles of the IHBs. It is inferred that the characteristics of these tubes (including the tight texture of their ‘walls’, the electron-richness of their cavities, and the possibility of expanding their size through the addition of more monomeric units) suggest potential interest for practical applications.

Ab Initio and Theoretical Study on Electron Transport through Polyene Junctions in between Carbon Nanotube Leads of Various Cuts

In this study we look into the interference effect in multi-thread molecular junctions in between carbon-nanotube (CNT) electrodes of assorted edges. From the tube end into the tube bulk of selected CNTs, we investigate surface Green’s function and layer-by-layer local density of states (LDOS), and find that both the cross-cut and the angled-cut armchair CNTs exhibit 3-layer-cycled LDOS oscillations. Moreover, the angled-cut armchair CNTs, which possess a zigzag rim at the cut, exhibit not only the oscillations, but also edge state component that decays into the tube bulk. In the case of cross-cut zigzag CNTs, the LDOS shows no sign of oscillations, but prominent singularity feature due to edge states. With these cut CNTs as leads, we study the single-polyene and two-polyene molecular junctions via both ab initio and tight-binding model approaches. While the interference effect between transport channels is manifested through our results, we also differentiate the contributions towards transmission from the bulk states and the edge states, by understanding the difference in the Green’s functions obtained from direct integration method and iterative method, separately.

The Jahn–Teller effect in the ground electronic state of the tetrafluoromethane cation before dissociation: a promoter of the anisotropic fragmentation

ABSTRACTThe role of multimode Jahn–Teller coupling effect on the anisotropic fragmentation of in its electronic state is investigated theoretically via an ab initio quantum dynamics study. The potential energy surfaces up to two-dimensions of nuclear coordinates are established from extensive electronic structure calculations. A higher order (seventh-order) diabatic vibronic coupling model Hamiltonian is necessary to mimic the ab initio potentials and thereby constructed. The theoretical results are in good agreement with experimental observations. A detail analysis of the relevant static aspects and the vibrational progressions under the structureless and broad vibronic band of are made. Present study suggests that the Jahn–Teller effect is operative before the dissociation of upon photoionisation and responsible for the experimentally measured anisotropic fragmentation in the electronic state of the title cation.

Surface vibrations in the T4 and H3 Pb phases on Si(111)

We present here a combined experimental Raman spectroscopy and ab initio theoretical study of the vibrational modes of the $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$ reconstructed SIC phase of Pb on Si(111) and discuss their relation to the atomic surface structure. The Raman response of the surface localized vibrational modes, in particular, is identified in the low-frequency spectral range (down to $15\phantom{\rule{3.33333pt}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1})$. We demonstrate that Raman spectroscopy is a very powerful approach to test atomic structures of surfaces and a valuable complement to standard surface analytics. While the calculated spectra of H3 and T4 are too similar to allow a discrimination of these phases, the good overall agreement to the measured Raman spectra enables a classification of the observed vibrational modes.

Ab initio molecular dynamics study of the reactions of allene cation induced by intense 7 micron laser pulses

ABSTRACTThe isomerisation and fragmentation of allene cation (H2C=C=CH2+) by short, intense laser pulses were simulated by Born-Oppenheimer molecular dynamics (BOMD) on the ground state potential energy surface using the B3LYP/6-31 + G(d,p) level of theory and a 10 cycle 7 µm cosine squared pulse with a maximum field strength of 0.07 au. Laser fields polarised along the C=C=C axis deposits an average of 150 kcal/mol in the molecule, compared to only 25 and 51 kcal/mol for perpendicular polarisations. Approximately 90% of the trajectories with the field aligned with the C=C=C axis underwent one or more structural rearrangement steps to form H2C=CH–CH+ (15%), H3CCCH+ (4%), cyclopropene cation (6%), and allene cation with rearranged hydrogens and carbons (47%). In addition, a variety of fragments including H2CCCH+ + H (10%), c-C3H3+ + H (7%), and HCCCH+ + H2 (2%) trajectories were produced after isomerisation. With the same amount of thermal energy, field-free BOMD shows good agreements with the BOMD with the field. However, RRKM calculations favour isomerisation to propyne cation and dissociation to HCCCH+ + H2. This suggests that for molecules in intense laser fields the energy in the intermediate isomers is not distributed statistically.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA)9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Dynamics of vibrational frequency fluctuations in deuterated liquid ammonia: roles of fluctuating hydrogen bonds and free ND modes

We present an ab initio molecular dynamics study of the roles of fluctuating hydrogen bonds and free ND modes in the dynamics of ND stretch frequency fluctuations in deuterated liquid ammonia. We have also looked at some of the other dynamical quantities such as diffusion and orientational relaxation and also structural quantities such as pair correlations and hydrogen bonding properties which are relevant in the current context. The time correlation function of ND stretch frequencies is found to decay with primarily two time scales: A short-time decay with a time scale of less than 100 fs arising from intermolecular motion of intact hydrogen bonds and also from fast hydrogen bond breaking and a longer time scale of about 500 fs which can be assigned to the lifetime of free ND modes. Unlike water, in liquid ammonia an ND mode is found to remain free for a longer period than it stays hydrogen bonded and this longer lifetime of free ND modes determines the long-time behaviour of frequency fluctuations. Our hole dynamics calculations produced results of vibrational spectral diffusion that are similar to the decay of frequency time correlation. Inclusion of dispersion corrections is found to make the dynamics slightly faster.

Separation of Pt(IV), Pd(II), Ru(III), and Rh(III) from chloride medium using liquid–liquid extraction with mixed imidazolium-based ionic liquids

ABSTRACTA reasonable project was presented for the extraction and separation of Pt(IV), Pd(II), Ru(III), and Rh(III) from the mixed imidazolium-based ionic liquids (ILs) [C6mim]Cl, [C6mim][NTf2], and [C6mim][DDTC]. Pt(IV) was first separated from other three platinum group metals with a mixture of [C6mim]Cl and [C6mim][NTf2]. Then, separation of Pd(II) and Ru(III) from Rh(III) was realized by changing the concentration of [C6mim][DDTC]. Back-extraction of Pt(IV), Pd(II), and Ru(III) from loaded hydrophobic phase and the recovery of Rh(III) in aqueous phase were also investigated. Mechanisms between Pd(II)/Ru(III) and [C6mim][DDTC] were further explored using ultraviolet spectrophotometry (UV-Vis), infrared spectrophotometry (FTIR), the method of continuous variations, ab initio quantum chemical studies, and X-ray crystallographic analysis. The results afford more directions for extracting and separating metals by introducing devisable functionalized group into ILs.

Structural, electronic, magnetic and thermodynamic properties of Ni1−xTixO alloys an ab initio calculation and Monte Carlo study

ABSTRACTStructural, electronic, magnetic and thermodynamic main features for Ni1−xTixO ternary alloys in rock-salt structure with Ti content in the range were studied using the full potential Linearized augmented plane wave (FP-LAPW) method within density functional theory. The exchange-correlation potential was calculated by the generalized gradient approximation. The analysis of the electronic density of states curves allowed the computation of the magnetic moments which are considered to lie along (010) axes. The thermodynamic stability of this alloy was investigated by calculating the excess enthalpy of mixing as well as the phase diagram. In addition, the Monte Carlo simulations have been exploited to calculate the transition temperature and magnetic coercive field in the alloy.

Ab Initio and DFT Study on Cyclophosphamide: Anticancer and Immunomodulating Agents

Cyclophosphamide is presently the most frequently used drug for antineoplastic chemotherapy. It has shown a great response in the treatment of human malignancies including leukemia, lymphoma, germ cell tumours, medulloblastomas, and carcinomas of the breast, lung, and cervix. Cyclophosphamide is also one of the most important immunosuppressive agents. This study investigates the quantum-chemical electronic properties of cyclophosphamide, as well as some of its metabolites, which are computed using ab-initio and DFT calculations. The interaction energy calculations between water molecules and the cyclophosphamide show how, in the solid state, the presence of water of crystallisation will make cyclophosphamide more stable over time. Atomic charges, dipole moment, frontier molecular orbitals, electrostatic potential isosurface, geometric parameters, and proton affinity on every nitrogen site enable the characterisation of the electronic properties and clearly illustrate the reactive sites that could be associated with this biologically important class of molecules.

The Effect of Platinum on β-NiAl/α-Al2O3 Interfacial Tensile Stress: A Combined Ab Initio DFT and Mechanics-Based Model Study

The beneficial effect of adding Pt in diffusion β-NiAl coating on reducing the tensile stress normal to the coating/α-Al2O3 scale interface has been investigated using a combination of ab initio density functional theory (DFT), phonon dispersion theory and mechanics-based interfacial stress modeling. The coefficient of thermal expansion (CTE) for Pt, β-NiAl and β-NiAl-6.25 at% Pt was calculated using the total energy DFT combined with the phonon dispersion theory. The calculated CTE of β-NiAl and β-NiAl-6.25 at% Pt and experimentally measured CTE of α-Al2O3 were used to evaluate the tensile stress of the undulated β-NiAl/α-Al2O3 and β-NiAl-6.25 at% Pt/α-Al2O3 interfaces resulting from the CTE mismatch between the coating and the oxide scale during cooling from elevated temperatures. It was found that the addition of Pt to β-NiAl is capable of lowering the interfacial tensile stress as a result of the reduced CTE of the Pt-modified β-NiAl coating, thus beneficial for improving thermal cyclic durability of the coating. The calculated results showed that the interfacial tensile stress is a function of oxide scale thickness and the interfacial wave amplitude and wavelength of an undulated interface. A thicker oxide scale and a rougher interface with a larger ratio of wave amplitude versus wavelength yield higher interfacial tensile stresses during thermal cycling. The addition of 6.25 at% Pt to β-NiAl coating reduces the coating/oxide scale interfacial tensile stress by about 27% over a wide range of scale thickness and interfacial wave amplitude and wavelength.

Ab initio structural studies of cyclobutylmethyl cations: effect of fluoroalkyl groups on the relative stability of the carbocations

Ab initio structural studies of cyclobutylmethyl cations: effect of fluoroalkyl groups on the relative stability of the carbocations

The dependence on ammonia pretreatment of N\u2212O activation by Co(II) sites in zeolites: a DFT and ab initio molecular dynamics study

This work is focused on the donor properties of cobalt-exchanged cationic sites in zeolites. It is based on cluster and periodic density functional theory modeling for relevant {[Co(II)(NH3)n]–NO} adducts, where Co(II) means a cobalt cation embedded either in a periodic model of chabasite (CHA) zeolite or in model clusters. NO stretching frequencies were derived from MD trajectories and compared to harmonic values from cluster calculations. By relating calculated NO frequencies to experimental FTIR spectra, it was shown that the forms of {Co(II)-NO} adducts comprising three or four ammonia co-ligands dominate the spectrum taken in ammonia-saturation conditions while forms with two NH3 ligands prevail under intermediate ammonia saturation. Finally, this work confirms the critical dependence of Co(II) activation ability towards NO upon the center donor properties, reinforced by ligation of strong donor ammonia ligands. However, strongly bound ligands appear also to compete with interaction of the center with the electron-rich framework, and a balance must be observed to maintain optimal activation ability.Graphical abstractA snapshot from MD trajectory showing a fragment of periodic framework with twoCo(II)–NO centers, bound to one framework oxygen and strongly coordinating three ammonia ligands with four others forming the second coordination sphere

How different is the borazine–acetylene dimer from the benzene–acetylene dimer? A matrix isolation infrared and ab initio quantum chemical study

ABSTRACTThe 1:1 dimer of borazine–acetylene has been studied for the first time, both experimentally and computationally. The borazine–acetylene dimer was trapped in Ar and N2 matrices, and studied using infrared spectroscopy. Our experiments clearly revealed two isomers of the borazine–acetylene complex, one in which the N–H of borazine interacted with the carbon of acetylene, and another in which the C–H of acetylene formed a hydrogen bond with a nitrogen atom of borazine. The formation of both isomers in the matrix was evidenced by shifts in the vibrational frequencies of the appropriate modes. Reassuringly, the experimental observations were corroborated by our computations using the second-order Møller–Plesset perturbation theoretic method and coupled-cluster singles, doubles and perturbative triples method in conjunction with different Dunning basis sets, which indicated both these isomers to be stable minima, with the N–H⋅⋅⋅C complex being the global minimum. Atoms-in-molecules and energy decomposition analysis were also carried out for the different isomers of the dimer. These studies reveal that replacing the three C–C linkages in benzene with three B–N linkages in borazine modifies the interaction in the dimer sufficiently, to result in a different potential energy landscape for the borazine–acetylene system when compared with the benzene–acetylene system.

Ab initio and TD-DFT study of the structural and spectroscopic properties of C30H10 as a new buckybowl

ABSTRACTIn this study, the structural and spectroscopic properties of the C30H10 as a sub-fullerene and a new buckybowl was carried out by quantum mechanical computations using B3LYP method and 6–311++G(d,p) basis set. All of the parameters were evaluated by density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were described which revealed different charge transfer possibilities for the molecule. The chemical shifts (δ, ppm) were predicted for 1H and 13C atoms using GIAO method. Natural bond orbital (NBO) analysis was carried out to picture the charge transfer between the localized bonds and lone pairs. The Fukui function (FF) for local reactivity of C30H10 was calculated and related discussions were done.

Effect of heterosubstituent and ring puckering angle on linear and nonlinear properties of exo-insaturated four-membered heterocycles, Y=CCH2CH2X: a comparative ab initio, DFT and semi-empirical study

ABSTRACTThe influence of heterosubstituent and ring puckering angle (ϕ) on electronic properties (μ, α, β and γ) of 16 four-membered heterocycles (1–16) were demonstrated theoretically using ab initio (HF and MP2), density functional theory (DFT) (PBE1PBE, SVWN5 and B3LYP) and semi-empirical (PM6 and PM3) treatments. Comparing the DFT and ab initio methods, these showed a similar description of electric dipole moment (μ) and polarisability (α) for each one of the studied heterocycles, with small differences in the prediction of α. The calculated hyperpolarisabilities (β and γ) are very sensitive to the quality of level theory, especially when the heterocycles contain phosphorus and sulphur. On the other hand, comparing with the rest of methods used, the semi-empirical calculations show significant deviations in the prediction of the different properties, and only are in agreement with the calculations of μ for the heterocycles that do not contain phosphorus or sulphur. In general, β and γ are more sensitive to the molecular geometry than μ and α. The dipole moment is determined by the heteroatom (X) within the ring, where the oxetanes and thietanes exhibit a minimum value of μ at planar conformations, while the azetidines and phosphetanes at axial conformations. All heterocycles show a minimum value of α at planar conformation, and their largest values are associated to conformations highly puckered. β exhibits an implicit relationship with the C = Y bond according to the conformational states. In addition, the X and Y heterosubstituents affect significantly the values of α, β and γ, observing the largest values for the phosphorus- and sulphur-containing heterocycles. Finally, considering the values obtained for α, β and γ, the studied heterocycles can represent an interesting unit for the design of new promising push–pull systems as donor or acceptor group.

Methodology of Nanomodified Binder Examination: Experimental and Numerical <i>Ab Initio</i> Studies

Feasibility of the sulfur-based construction materials is caused by properties, availability and low cost of sulfur. There exist numerous ways to improve the operational properties, including the ways that are based on nanotechnology, and ab initio (quantum chemistry) studies. Unfortunately, both application and verification of numerical simulation within the same research are quite complex. In the present case study we present typical scheme of survey involving both experimental and numerical studies. As a test subject we have selected orthorhombic sulfur crystals grown from the solution in toluene. It was clearly shown that good correspondence between experimental and numerical results can be achieved for offered methodology; Raman shifts for isolated S8 molecule mostly correspond to the shifts of sulfur crystal. Computed frequencies for all primary modes are close to the experimental data. Similar correspondences can serve as proofs of conformity between unknown molecular structures in nanomodified sulfur-based material and selected structural models