Theab Initio Research Articles

Vibrational and Raman Spectroscopic Study of Cubic Boron Nitride Under Pressure Using Density Functional Theory

Pressure-dependent mechanical, vibrational and Raman spectroscopic study of the cubic boron nitride in context of recent experimental Raman spectroscopic has been performed using theab initio calculations based on density functional theory. Detailed analysis of the pressure-dependent mechanical and phonon properties shows that the pressure significantly affects the elastic constants and phonon frequencies. There is a systematic variation of elastic properties with pressure while a polynomial expression is used to fit the pressure dependence of the Raman shift. The longitudinal optical–transverse optical (LO-TO) splitting reduces with pressure, and the intensity of both LO and TO peaks start diminishing after 750 GPa. The phonon dispersion curves up to 1000 GPa indicate its dynamical stability. The lower slope of frequency versus pressure for the LO and TO modes at higher pressures suggests its use for pressure calibration at higher pressures.

XMDYNandXATOM: versatile simulation tools for quantitative modeling of X-ray free-electron laser induced dynamics of matter

Rapid development of X-ray free-electron laser (XFEL) science has taken place in recent years owing to the consecutive launch of large-scale XFEL instruments around the world. Research areas such as warm dense matter physics and coherent X-ray imaging take advantage of the unprecedentedly high intensities of XFELs. A single XFEL pulse can induce very complex dynamics within matter initiated by core-hole photoionization. Owing to this complexity, theoretical modeling revealing details of the excitation and relaxation of irradiated matter is important for the correct interpretation of the measurements and for proposing new experiments.XMDYNis a computer simulation tool developed for modeling dynamics of matter induced by high-intensity X-rays. It utilizes atomic data calculated by theab initio XATOMtoolkit. Here these tools are discussed in detail.

Track structure of protons and other light ions in liquid water: Applications of the LIonTrack code at the nanometer scale

The LIonTrack (Light Ion Track) Monte Carlo (MC) code for the simulation of H(+), He(2+), and other light ions in liquid water is presented together with the results of a novel investigation of energy-deposition site properties from single ion tracks. The continuum distorted-wave formalism with the eikonal initial state approximation (CDW-EIS) is employed to generate the initial energy and angle of the electrons emitted in ionizing collisions of the ions with H2O molecules. The model of Dingfelder et al. ["Electron inelastic-scattering cross sections in liquid water," Radiat. Phys. Chem. 53, 1-18 (1998); "Comparisons of calculations with PARTRAC and NOREC: Transport of electrons in liquid water," Radiat. Res. 169, 584-594 (2008)] is linked to the general-purpose MC code PENELOPE/penEasy to simulate the inelastic interactions of the secondary electrons in liquid water. In this way, the extended PENELOPE/penEasy code may provide an improved description of the 3D distribution of energy deposits (EDs), making it suitable for applications at the micrometer and nanometer scales. Single-ionization cross sections calculated with the ab initio CDW-EIS formalism are compared to available experimental values, some of them reported very recently, and the theoretical electronic stopping powers are benchmarked against those recommended by the ICRU. The authors also analyze distinct aspects of the spatial patterns of EDs, such as the frequency of nearest-neighbor distances for various radiation qualities, and the variation of the mean specific energy imparted in nanoscopic targets located around the track. For 1 MeV/u particles, the C(6+) ions generate about 15 times more clusters of six EDs within an ED distance of 3 nm than H(+). On average clusters of two to three EDs for 1 MeV/u H(+) and clusters of four to five EDs for 1 MeV/u C(6+) could be expected for a modeling double strand break distance of 3.4 nm.

Towards an elastic model of wurtzite AlN nanowires

Starting with ab initio calculations of AlN wurtzite [0001] nanowires with diameters up to4 nm, a finite element method is developed to deal with larger nanostructures/nanoparticles.The ab initio calculations show that the structure of the nanowires can be well representedby an internal part with AlN bulk elastic properties, and one atomic surface layer with itsown elastic behavior. The proposed finite element method includes surface elements withtheir own elastic properties using surface elastic coefficients deduced from theab initio calculations. The elastic properties obtained with the finite elementmodel compare very well with those obtained with the full ab initio calculations.

Finding the lowest-energy crystal structure starting from randomly selected lattice vectorsand atomic positions: first-principles evolutionary study of the Au–Pd, Cd–Pt, Al–Sc,Cu–Pd, Pd–Ti, and Ir–N binary systems

Two types of global space-group optimization (GSGO) problems can be recognized in binary metallicalloys AqB1−q: (i) configuration search problems, where the underlying crystal lattice is known and theaim is finding the most favorable decoration of the lattice by A and B atoms and (ii)lattice-type search problems, where neither the lattice type nor the decorations aregiven and the aim is finding energetically favorable lattice vectors and atomicoccupations. Here, we address the second, lattice-type search problem in binaryAqB1−q metallic alloys, where the constituent solids A and B have different lattice types. We tacklethis GSGO problem using an evolutionary algorithm, where a set of crystal structures withrandomly selected lattice vectors and site occupations is evolved through a sequence ofgenerations in which a given number of structures of highest LDA energy are replaced bynew ones obtained by the generational operations of mutation or mating. Each newstructure is locally relaxed to the nearest total-energy minimum by using theab initio atomic forces and stresses. We applied this first-principles evolutionaryGSGO scheme to metallic alloy systems where the nature of the intermediate A–Bcompounds is difficult to guess either because pure A and pure B have different latticetypes and the (i) intermediate compound has the structure of one end-point(Al3Sc,AlSc3,CdPt3), or (ii) none of them (CuPd, AlSc), or (iii) when the intermediatecompound has lattice sites belonging simultaneously to a few types (fcc, bcc)(PdTi3). The method foundthe correct structures, L12 type for Al3Sc, D019 typefor AlSc3,‘CdPt3’ typefor CdPt3, B2 type for CuPd and AlSc, and A15 type forPdTi3. However, in such stochastic methods, success is not guaranteed, since manyindependently started evolutionary sequences produce at the end differentfinal structures: one has to select the lowest-energy result from a set of suchindependently started sequences. Interestingly, we also predict a hitherto unknown(P 2/m) structure of thehard compound IrN2 with energy lower than all previous predictions.

Simulation of Helium Behaviour in Titanium Crystals UsingMolecular Dynamics

The behaviour of helium in Ti crystals at 300 K has been investigatedby means of the molecular dynamics. The study is focused on theinfluences of He–Ti interaction on the aggregation of helium atoms inthe substrate. When a Born–Mayer potential is used to describe theHe–Ti interaction, the He atoms are unable to cluster with each otherdue to the weak bridge barrier that cannot trap the helium atoms,Whereas using a He–Ti potential that is constructed by fitting theab initio pairwise He–Ti potential, the clustering of He atomscan be observed. The results indicate that suitable He–Ti potentialplays an important role in the formation of He clusters in metals.Moreover, it is noted that the shape of the formed He cluster is irregular,and the produced defect prefers to congregating on one side of the Hecluster rather than spreading symmetrically around it.

Realization of prediction of materials properties byab initio computer simulation

Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest supercomputer efficiently. Therefore, it is very difficult to simulate realistic materials with grain boundaries and important reactions like diffusion in materials. To improve this situation, two ways have been invented. One way is to upgrade approximations to match the necessary levels according to inhomogeneous electron gas theory beyond the present day standard, i.e. local density approximation (LDA). The reason is simply that the system we are interested in is composed of many particles interacting with Coulomb forces governed by quantum mechanics. (Complete knowledge is available, and only what we should do is to make better approximations to explain the phenomena!). Another is to extract the necessary parameters from theab initio calculations on systems with limited number of atoms, and apply these results into cluster variation, direct, or any other sophisticated methods based on classical concepts such as statistical mechanics. In this paper, several typical examples recently worked out by our research group are introduced to indicate that these methodologies are actually possible to be successfully used to predict materials properties before experiments based on the present day state-of-art supercomputing systems. It includes scientific visualization of the results ofab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube, tight-binding calculation of single electron conductance properties in nanotube to create nano-scale diode virtually by computer, which will be a base of future nanoscale electric device in nanometer size, Li + H reaction without Born-Oppenheimer approximation, structural phase transitions in perovskite materials under very high pressure in earth by direct method, and prediction of wavelength of emitted light from Na clusters with GW (G = Green function-vertex, W = screened Coulomb interaction) approximation.

Novel aromatic borafluorole, fluoraborabenzene and diborafluorabenzene heterocyclic systems: an ab initio study

Theab initio[MP2(fu)/6-311+G**] and DFT (B3LYP/6-311+G**) calculations predict aromatic stabilization of the planar structures of borafluorole, fluoraborabenzene and diborafluorabenzenes, boron-containing heterocycles with hypercoordinated fluorine centres.

Structures and stability of (HAlNH n (n=1–15)

The geometries, electronic states, vibrational spectra and thermodynamic properties for (HAINH) n clusters withn=1–15 have been investigated using theab initio DFT/B3LYP method with basis sets 6-31G* and their ground state structures obtained. Comparison of the (HAlNH) n with (AlN) n clusters shows that the skeletons of (HAlNH) n consist of four-membered and six-membered rings made of Al-N bonds, and either Al or N atom forms four bonds in which three ones are Al-N bonds and the rest is Al-H or N-H bond. The number of Al-N bonds of (HAlNH) n is equal to that of (AlN) n . The magic number regularity of (HAlNH) n isn=2, 4, 6, 8, etc., all of which are even numbers.

Anab initio quantum-chemical study of proton addition to F-, Ch3-, and CF3-substituted ethylene derivatives

Protonated forms of the molecules of ethylene derivatives with the general formula C2X2Y2 (X=Y=H) (1), F (2), CH3 (3) CH3 (4); X=F, Y=H:cis-(5)trans- (6)) were calculated by theab initio MP2/6-31 G* method with full geometry optimization. The minima and saddle points located on the potential energy surface (PES) of the protonated ethylene molecule correspond to the stationary states and transition states of proton migration, respectively. The stationary states are characterized by a nonclassical geometry of carbocations similar to that of π-complexes, whereas the transition states have a classical structure. Unlike1, the carbocations of molecules2–6 have the classical structure. The saddle points on the PES of the ethylene derivatives correspond to the structures of the π-complex type, which are the transition states of proton migration between the C atoms of the ethylene bond. The barrier to rotation about, the C−C bond depends essentially on the substituent nature.

Spin-dependent electron momentum density in Fe3Si andFe3Al

Circularly polarized synchrotron radiation of energy 200 keV has been used tostudy the spin dependent electron momentum distributions in Fe3Al and Fe3Si single crystals at room temperature throughmagnetic Compton profile measurements. The experiments were carried out forthe crystallographic directions [100], [110] and [111] in Fe3Si, and [100] and [111] in Fe3Al. These resultsshow that there is a more significant negative conduction electron spinpolarization in both alloys than neutron data indicate and it is similar tothat in pure iron. The overall characteristics of the experimental magneticCompton profiles, as well as directional anisotropies, were found to bequalitatively similar for both compounds; however the anisotropy is higher inthe case of Fe3Si. The majority and minority spin band profileshave been extracted and show that large anisotropies are associated with thelatter. Their calculated anisotropy at low momenta was fully confirmed. Theab initio KKR calculation reproduces the Fe3Si profilesrelatively well, but a `fixed-spin moment approach' was needed in order todescribe the Fe3Al spin density momentum distribution.

Interaction of O+ ion with water molecules: A quantum-chemical study

The interaction of O+ ion with several (from one to four) water molecules was studied by theab initio (UMP4/4-31G*) and semiempirical (AM1) quantum-chemical methods. It was found that the energy of binding the O+ ion to the first water molecule is appreciably higher than those of binding to the subsequent water molecules. In the complex with a water molecule, whose structure corresponds to that of water oxide, the O+ ion retains high reactivity. The barrier to the transfer of O+ ion to another water molecule is much lower than the barrier to analogous transfer of O atom from the molecule of water oxide, despite the lower dissociation energy of the H2O−O bond. Consideration of subsequent interactions with water molecules leads to an increase in the barrier to the transfer of O+ ion. The doublet and quadruplet excited states of the O++2 H2O system were also studied. In these cases, the formation energies are well described by the ion-dipole model.

Stabilization of nonclassical types of valence bond orientation at the carbon atom in organoboron compounds

The complete topological structure of the potential energy surface (PES) of methane in the inversion region was studied by theab initio CCD(full)/6-311++G** method. The necessity of taking into account nuclear motions was shown. Penta- and hexacoordination of carbon atoms in boron-containing organic compounds was investigated by theab initio MP2(full)/6-31G** and MP2(full)/6-311++G** methods. The CB4H4Li2, CB6N2H2, and CB6O2 systems containing hexacoordinated carbon atoms correspond to rather deep minima on the relevant PES and can be the subject of synthetic studies. According to theab initio calculations, pyramidal boron-containing systems with hypercoordinated carbon atoms, which fulfill the “8e rule,” also correspond to rather deep PES minima and can be detected experimentally.

Canab initio simulation really predict properties of materials prior to experimental

In this paper we have presented all-electron full-potentialab initio simulation method with introduction of mixed-basis, and have cited several typical examples which indicate that it is possible to predict properties of materials prior to experimental. Based on theab initio calculation of the total energy, cluster variation, and direct methods function, it is possible to bridge the limited scheme of theab initio treatment to real complex materials. Furthermore, to overcome the limited computer power, we have developed parallel processing codes and tested their efficiencies as well.

Intramolecular nucleophilicS N 2 substitution at the tetrahedral carbon atom: Anab initio study

Pentacoordination of carbon atom in bicyclic organic compounds of the pentalene type was studied by theab initio RHF/6-31G** and MP2(full)/6-31G** methods. It was shown that intramolecularSN2 reactions with energy barriers within the energy scale of NMR spectroscopy can occur in systems in which a linear orientation of the attacking and leaving groups is realized. The barrier to the intramolecular nucleophilic substitution reaction in 2,3-dihydro-3-formylmethylenefuran is 36.9 (RHF) and 27.7 kcal mol−1 (MP2) and decreases to 16.4 and 19.4 kcal mol−1, respectively, in the case of diprotonation at the O atoms in this system. For model pentalene type compounds containing electron-deficient B atoms in the ring, theab initio calculations predict a further decrease in the barrier height (down to less than 10 kcal mol−1).

Pentacoordination of boron, carbon, aluminum, and silicon atoms in organic compounds: Anab initio study

Pentacoordination of boron, carbon, aluminum, and silicon atoms in bicyclic organic compounds of the pentalene type was studied using theab initio RHF/6-31G** and MP2(full)/6-31G** methods. It was shown that the ability of the atom to form pentacoordinate structures increases on going from B to Al and from C to Si atom,i.e. as the number of the element of Groups IIIA and IVA of the periodic system increases. At the same time, the reverse tendencies are observed in the 2nd and 3rd periods of the periodic system,viz., the ability of the atom to form pentacoordinate structures increases on going from C to B and from Al to Si atom.

Pathways of the reactions of nucleophilic addition of H2O and HF molecules to formaldehyde in the gas phase and in the complex with formic acid:ab initio calculations

The gradient pathways of the reactions of nucleophilic addition of H2O and HF molecules to formaldehyde in the gas phase and in the XH…H2CO…HC(O)OH complex (X=OH, F) were calculated by theab initio RHF/6-31G**, MP2(fc)/6-31G**, and MP2(full)/6-311++G** methods. Both reactions proceed concertedly. The formation of H-bonded bimolecular pre-reaction complexes is the initial stage of the gas-phase reactions; at the same time, no indications of the formation of stable π-complexes were found on the potential energy surfaces of systems under study. The calculated energy barriers to the gasphase reactions exceed 40 kcal mol−1, while those to reactions in the complex XH…H2CO…HC(O)OH (X=OH, F) become more than halved.

Structure and coordination of organometallic groups on a chemically modified SiO2 surface

The structural, electronic, and energy parameters of the metal-containing clusters (H3SiO)3Si−O−XMe n (X=H, B, Al, or Zn;n=0, 1, or 2), which model organometallic groups on a SiO2 surface modified with B-, Al-, and Zn-containing alkyls, have been studied by quantum-chemical methods. Full geometry optimization for these clusters was carried out by the SCF MO LCAO method taking into account the electron correlation within the frameworks of the MP2 and B3LYP schemes using the 6-31G(d) (6-311G(d) for Zn) basis set. The effect of the crystal environment was taken into account in calculations of siliconoxygen clusters containing 10 and 30 silicon atoms using theab initio SCF/6-31G(d) and semiempirical MNDO-PM3 methods. Various modes of coordination and interactions of organometallic groups with oxygen atoms of surface groups were studied. For the organoaluminum group on the surface, two stable conformations were found, namely, the three-coordinate structure with the chain −O−AlMe2 ligand and the four-coordinate (quasicyclic) structure with the Al atom that forms two nonequivalent bonds with the O atoms at the same Si atom. The four-coordinate structure is energetically more favorable. No stable structures were found for the organoboron and organozinc fragments.

Matrix IR-spectroscopic and quantum-chemical study of difluorostannylene complexation with dinitrogen

Complexes of difluorostannylene with dinitrogen of composition 1∶1 and 1∶2 were stabilized in Ar matrix (12 K) and characterized by IR spectra. The bands at 588, 565, and 583, 557 cm−1, respectively, were assigned to these complexes. Potential energy surfaces of the systems SnF2+N2 and SnF2+2N2 were studied by theab initio MP2/3-21G(d2)//HF/3-21G(d2) method using the basis set including polarization functions at Sn, F, and N atoms. Equilibrium structures of the complexes haveC s andC 2v symmetry and correspond to coordination of lone electron pairs of nitrogen molecules with vacant p-AO of the carbenic center. The calculated complexation energies are equal to 4.6 and 8.9 kcal mol−1, respectively. Based on results of quantum-chemical calculations an interpretation of the IR spectra of the complexes was given and it was shown that cycloaddition of SnF2 to a triple N≡N bond with formation ofcyclo-SnF2N2 is energetically unfavorable. The absorption band belonging to SiF4·N2 complex in Ar matrix was detected and assigned.

Pathways of the reaction of nucleophilic addition of ammonia to formaldehyde in the gas phase and in the complex with formic acid:ab initio calculations

The gradient pathways of the reaction of nucleophilic addition of ammonia to formaldehyde were calculated for free molecules and in the NH3...H2CO...HC(O)OH complex by theab initio RHF/6-31G**, MP2(fc)/6-31G**, and MP2(full)/6-311++G** methods. Both reactions proceed concertedly. In the first case, the reaction successively passes through two transitional states with an energy barrier exceeding 35 kcal mol−1. In the case of the complex with formic acid, the reaction follows a conventional pathway, although its activation barrier calculated by the RHF/6-31G** and MP2(fc)/6-31G** methods decreases to 12.6 and 3.8 kcal mol−1, respectively.