Ab initio molecular dynamics — Applications to the molecular and solid state physics of phosphorus

Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, first principles MD or Car-Parrinello method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics/chemistry (liquid phosphorus). Dynamical, finite temperature, simulations deriving interatomic forces from state-of-the-art density functional calculations represent a substantial advance over both (i) traditional pointwise total energy and electronic band structure calculations and (ii) classical MD simulations with empirical or semi-empirical forces, and have already yielded qualitatively new insights in several fields.     

Ab initio studies on the pyrolysis mechanism of 2-haloacetic acids in the gas phase

The dehydrohalogenation mechanism of 2-haloacetic acids (XCH2CO2H, X=F, Cl and Br) has been studied theoretically by HF/3-21G and AM1 methods. The results indicate that these reactions are most probably proceeded in terms of a polar five-membered cyclic transition state in the gas phase. Their microscopic processes are beleived to be a stepwise reaction and the rate-determining step is the first one. By comparing the energy barriers of different 2-haloacetic acids, it can be realized that 2-fluoroacetic acid is easier to react than 2-chloroacetic and 2-bromoacetic acids.     

Ab initio simulation of the photoelectron spectra of HCO− and DCO−

Large scale, vibrational CI calculations using a global ab initio potential energy surface are used to calculate multidimensional Franck-Condon overlaps from the ground vibrational state of HCO⁻ and DCO⁻ to all final bound and several quasibound vibrational states of HCO and DCO. The resulting Franck-Condon spectra are compared with recent experimental photoelectron spectra of HCO⁻ and DCO⁻.     

Ab initio calculations of the structural and elastic properties of CoSi2

Under GGA, the geometry, energy, electronic structure, and elastic properties of the CoSi₂ have been investigated by using ab initio plane-wave ultrasoft pseudopotential method. The calculated equilibrium lattice parameter a and elastic stiffness constants c ₁₁, c ₁₂, and c ₄₄ are in better agreement with the experimental values than those obtained by both the VAMP and FLAPW with LDA. For engineering and technological applications, the isotropic elastic properties, including the shear modulus G, the bulk modulus B, Young’s modulus E, and Poisson’s ratio , are also calculated for polycrystalline CoSi₂ with Voigt, Reuss, and Hill approximations. The lower Poisson’s ratio of 0.327 means an increase in the volume is associated with the uniaxial tensile deformation and the higher ratio of bulk modulus to shear modulus B/G of 2.56 indicates the ductility of CoSi₂ which is in accordance with the metallic property of CoSi₂ obtained by the density of states.     

Ab initio Calculation of Intermolecular Dispersion Energy and Induction Energy of Nitramide Dimer

The dispersion energies, induction energies and their exchange counterparts (exchange-dispersion and exchange-induction energies) between two interacting nitramide molecules at several separations are derived based upon symmetry-adapted perturbation theory (SAPT). The results show that (1) the effect of intramonomer electron correlation on dispersion energies and induction energies for nitramide dimer system is remarkable especially in the region near the van der Waals minimum distance (0.42 nm). (2) At smaller separations the dispersion energies and the induction energies are largely quenched by their exchange counterparts, and this case in induction interaction is much more remarkable than in dispersion interaction. (3) Since at shorter distances there exists the strong short-range interaction due to electron transfer which quickly decays and even disappears at larger separations, the two different R-dependency formulae of induction energies were found: one is ca. R^-12.7 at short distances, and the other ca. R^-7.0 at large separations. The latter R-dependency is similar to that (ca.R^-7.2) of dispersion. (4) In the case of strong polar interaction existing in nitramide dimer, the “true“ induction correlation terms of higher order than ^1Eind^(22) may be important.     

Ab initio VB Studies of the Ground and Low-lying Excited States of BeH and BH

A scheme has been proposed to classify valence bond(VB) wave functions for the calculations of ground and excited states,according to the symmetry properties of one-electron orbitals which are involved in the construction of VB wave functions.This scheme is illustrated by the examples of BeH and BH.Ab initio VB computations of these two test molecules in combination with the present classification scheme give reliable results.For example,calculation results show that the state C2∑ of BeH is stable,with the bonding energy 0.87 eV and bond length 0.238nm,which are in good agreement with those obtained by Gerratt et al.The bonding features of ground and low-lying excited states of BeH and BH are discussed.     

Ab initio Study on the Tautomerization Mechanism and the Kinetics of Formamide

The tautomerism of formamide has been investigated by ab initio calculation using RHF/4-31G basis set. The change in some physical properties along the reaction path is presented. In the study of molecular reaction kinetics, we have calculated all the kinetic parameters according to statistical thermodynamics and transition state theory. The combination of kinetics analysis with IRC analysis has indicated that the tautomerism is concerted but the geometric changes are nonsynchronous; the lifetime of the transition state is short and the transition state is tight type; the formamide is more stable than formimidic acid; the kinetic rate constant of backward reaction is larger than that of the forward reaction in the range of temperature studied.     

Ab initio investigation on the structures and spectra of the firefly luciferin

The ground state (S0) geometry of the firefly luciferin (LH2) was optimized by both DFT B3LYP and CASSCF methods. The vertical excitation energies (Tv) of three low-lying states (S1, S2, and S3) were calculated by TD-DFT B3LYP//CASSCF method. The S1 geometry was optimized by CASSCF method. Its Tv and the transition energy (Te) were calculated by MS-CASPT2//CASSCF method. Both the TD-DFT and MS-CASPT2 calculated S1 state Tv values agree with the experimental one. The IPEA shift greatly affects the MS-CASPT2 calculated Tv values. Some important excited states of LH2 and oxyluciferin (oxyLH2) are charge-transfer states and have more than one dominant configuration, so for deeply researching the firefly bioluminescence, the multireference calculations are desired.     

Ab initio study of mechanism of cycloaddition reaction between H2Ge = Ge: and acetone

The mechanism of the cycloaddition reaction between singlet H₂Ge = Ge: and acetone has been investigated with CCSD(T)//MP2/6-31G* method. From the potential energy profile, it could be predicted that the reaction has two competitive dominant reaction pathways. The reaction rule presented is that the two reactants firstly form a four-membered Ge-heterocyclic ring germylene through the [2 + 2] cycloaddition reaction. Because of the 4p-unoccupied orbital of Ge atom in the four-membered Ge-heterocyclic ring germylene and the π-orbital of acetone forming a π → p donor–acceptor bond, the four-membered Ge-heterocyclic ring germylene further combines with acetone to form an intermediate. Because the Ge atom in intermediate happens sp³ hybridization after transition state, then, intermediate isomerizes to a spiro-Ge-heterocyclic ring compound via a transition state. Simultaneously, the ring strain of the four-membered Ge-heterocyclic ring germylene makes it isomerize to a twisted four-membered ring product.     

Ab initio density functional theory: the best of both worlds?

Density functional theory (DFT), in its current local, gradient corrected, and hybrid implementations and their extensions, is approaching an impasse. To continue to progress toward the quality of results demanded by today's ab initio quantum chemistry encourages a new direction. We believe ab initio DFT is a promising route to pursue. Whereas conventional DFT cannot describe weak interactions, photoelectron spectra, or many potential energy surfaces, ab initio DFT, even in its initial, optimized effective potential, second-order many-body perturbation theory form [OEP (2)-semi canonical], is shown to do all well. In fact, we obtain accuracy that frequently exceeds MP2, being competitive with coupled-cluster theory in some cases. Furthermore, this is accomplished within a relatively fast computational procedure that scales like iterative second order. We illustrate our results with several molecular examples including Ne2,Be2,F2, and benzene.     

Ab initio study of long-range electron transfer between biphenyl anion radical and naphthalene

After the separation of the donor, the aeceptor, and the σ-type bridge from the π-σ-π system, the geometries of biphenyl, biphenyl anion radical, naphthalene, and naphthalene anion radical are optimized, and then the reorganization energy for the intermolecular electron transfer (ET) at the levels of HF/4-31G and HF/DZP is calculated. The ET matrix elements of the self-exchange reactions of the π-σ-π systems have been calculated by means of both the direct calculation based on the variational principle, and the transition energy between the molecular orbitals at the linear coordinate R=0.5. For the cross reactions, the ET matrix element and the geometry of the transition state are determined by searching the minimum energy splitting △_(min) along the reaction coordinate. In the evaluation of the solvent reorganization energy of the ET in solution, the Marcus' two-sphere model has been invoked. A few of ET rate constants for the intramolecular ET reactions for the π-σ-π systems, which contain     

TEM study of band-like cellulose assemblies produced by Acetobacter xylinum at 4 °C

Two kinds of band-like cellulose assemblies, coarse and densestructures, are produced in Hestrin–Schramm medium at 4 °Cusing smooth colonies isolated from Acetobacter xylinumATCC23769, whereas ribbon cellulose assemblies are produced by the samecoloniesat 28 °C. The dense and the coarse band-like assembliesconsist of many strand-like cellulose entities (strands) and areextruded perpendicularly to the long axis of the bacterial cell. In an earlystage of incubation at 4 °C, the dense band-like assembly isproduced and the number of strands decreases gradually with increasingincubation time at 4 °C, probably because the number of activeTC subunits decreases as a result of the low-temperature shock for thebacteria.In contrast, the coarse band-like assembly is clearly observed after about 1h of incubation at 4 °C. The number of strands inthe coarse band-like assembly is about one third of that of the dense band-likeassembly and does not change during the incubation time of about 6h. In the selected-area electron diffraction (ED) experiment, thedense band-like assembly gives crystalline reflections corresponding to thecellulose II type crystal, while the coarse band-like assembly does not giveanycrystalline reflections under the same ED conditions.     

Polymerization and decomposition of terephthaloyl chloride and p-phenylenediamine at 500 °C

In order to synthesize the high temperature solid lubricating film by gas-phase polymerization at 500?°C with two kinds of gasified monomers for use in airplane and rocket engines, the polymerizing activity of terephthaloyl chloride (TPC) and p-phenylenediamine (PPD) at 500?°C and their polymerized product poly-p-phenyleneterephthamide (PPTA) as well as its decomposed solid residues were researched. It was proved by FT-IR and ¹HNMR on the solid residues after the 10?min experiment of the both monomers in muffle furnace at 500?°C and PPTA synthesized by conventional method that at 500?°C the polymerization tendency of these monomers should trump their decomposition tendency. The solid residues after the 10?min experiment mainly consisted of polymerized products which would decline as the experimental period increases, while the content of decomposed and carbonized products would raise. FT-IR and elemental analysis revealed a similar structure of the solid residues after the both monomers or PPTA calcined for 60?min at 500?°C, which further demonstrated the polymerized products would degrade, decompose and carbonize after the prophase polymerization. Finally, effects of experimental temperature and monomers molar ratio on amounts and structures of the solid residues were discussed to propose preliminary mechanisms of polymerization and decomposition.     

Antioxidant properties of β-carotene isomers and their role in photosystems: insights from Ab initio simulations

In this work we investigate the effect of cis isomerizations and conformational changes on the antioxidant activity of β-carotene, one of the most important pigments in nature. The electrodonating (ω(-)) and electroaccepting (ω(+)) powers of the most relevant isomers of β-carotene are first evaluated in polar and nonpolar solvents using density functional theory (DFT), and these quantities are then used to establish an antioxidant scale of the isomers. The electrodonating power, which is directly related to the antioxidant activity, is shown to provide a very good correlation with the experimental data. Next, we compute the intermediate twisted structures of the β-carotene isomers generated by partial rotation of every single bond in the polyenic chain. The electrodonating and electroaccepting powers are evaluated for each of these intermediate structures along with their maximum absorption wavelengths, which are computed using time-dependent DFT (TD-DFT). The trends observed for both the electrodonating power and the maximum absorption wavelength can be rationalized in terms of the effective conjugated chain length of the structure resulting from single bond rotations. The results obtained are used to analyze the conformational distribution of β-carotene in the well-resolved photosystem I (PS-I) of purple cyanobacteria. It is then shown that the isomers present in this photosystem are those having the lowest calculated relative energies and that those with enhanced antioxidant activity are preferentially located in the inner core of the protein complex.     

Ab initio study of tautomerism and hydrogen bonding of β-carbonylamine in the gas phase and in water solution

All the possible conformations of the three tautomeric isomers of simple β-carbonylamine were fully optimized at ab initio MP2/6-31G** and B3LYP/6-31G** levels in order to determine the conformational equilibrium and the energies of the O—H···N and O···H—N hydrogen bridges. For the most interesting conformations, further calculations in water solution were also carried out. It was found that carbonylamine is the most stable tautomer, followed by enolimine and carbonylimine. This order of stability does not change in solution. O—H···N is the strongest hydrogen bridge, but in solution its energy as well as that of the O···H—N one are dramatically lowered. The deprotonation energy was also calculated and discussed. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 5 June 2000     

Ab initio calculations for the potential curves and spin–orbit coupling of Mg2

 The ground state and several low-lying excited states of the Mg₂ dimer have been studied by means of a combination of the complete-active-space multiconfiguration self-consistent-field (CASSCF)/CAS multireference second-order perturbation theory (CASPT2) method and coupled-cluster with single and double excitations and perturbative contribution of connected triple excitations [CCSD(T)] scheme. Reasonably good agreement with experiment has been obtained for the CCSD(T) ground-state potential curve but the dissociation energy of the only experimentally known A¹Σ _u ⁺ excited state of Mg₂ is somewhat overestimated at the CASSCF/CASPT2 level. The spectroscopic constants D _e, R _e and ω_e deduced from the calculated potential curves for other states are also reported. In addition, some spin–orbit matrix elements between the excited singlet and triplet states of Mg₂ have been evaluated as a function of internuclear separation. Received: 10 May 2001 / Accepted: 15 August 2001 / Published online: 30 October 2001     

Ab initio Calculation and Kinetic Study for the Abstraction Reaction of H with Sihcl3

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