First principles NMR calculations by fragmentation

The nuclear magnetic shielding tensor is a molecular property that can be computed from first principles. In this work we show that by utilizing the fragmentation approach, one is able to accurately compute this property for a large class of molecules. This is of great significance because the computational expense required in the evaluation of the shielding tensor for all nuclei in a large molecule is now subject to near linear scaling. On the basis of previous studies and this work, it is also very likely that all molecular properties that can be expressed as derivatives of the total energy of the system are also amenable to accurate evaluation via fragmentation. If only the chemical shifts for nuclei in a small part of a large molecule are of interest, then only those molecular fragments containing those nuclei need to have their shielding tensors evaluated. Further, the fragmentation approach allows one to construct a database of molecular fragments that could, in principle, be used in the NMR characterization of molecules and at the same time provide possible three-dimensional representations of these molecules.     

First principles study of magnetism in nanographenes

Magnetism in nanographenes [also known as polycyclic aromatic hydrocarbons (PAHs)] is studied with first principles density functional calculations. We find that an antiferromagnetic (AFM) phase appears as the PAH reaches a certain size. This AFM phase in PAHs has the same origin as the one in infinitely long zigzag-edged graphene nanoribbons, namely, from the localized electronic state at the zigzag edge. The smallest PAH still having an AFM ground state is identified. With increased length of the zigzag edge, PAHs approach an infinitely long ribbon in terms of (1) the energetic ordering and difference among the AFM, ferromagnetic, and nonmagnetic phases and (2) the average local magnetic moment at the zigzag edges. These PAHs serve as ideal targets for chemical synthesis of nanographenes that possess magnetic properties. Moreover, our calculations support the interpretation that experimentally observed magnetism in activated carbon fibers originates from the zigzag edges of the nanographenes.     

First principles molecular dynamics of molten NaCl

First principles Hellmann-Feynman molecular dynamics (HFMD) results for molten NaCl at a single state point are reported. The effect of induction forces on the structure and dynamics of the system is studied by comparison of the partial radial distribution functions and the velocity and force autocorrelation functions with those calculated from classical MD based on rigid-ion and shell-model potentials. The first principles results reproduce the main structural features of the molten salt observed experimentally, whereas they are incorrectly described by both rigid-ion and shell-model potentials. Moreover, HFMD Green-Kubo self-diffusion coefficients are in closer agreement with experimental data than those predicted by classical MD. A comprehensive discussion of MD results for molten NaCl based on different ab initio parametrized polarizable interionic potentials is also given.     

First principles semiclassical calculations of vibrational eigenfunctions

Vibrational eigenfunctions are calculated on-the-fly using semiclassical methods in conjunction with ab initio density functional theory classical trajectories. Various semiclassical approximations based on the time-dependent representation of the eigenfunctions are tested on an analytical potential describing the chemisorption of CO on Cu(100). Then, first principles semiclassical vibrational eigenfunctions are calculated for the CO(2) molecule and its accuracy evaluated. The multiple coherent states initial value representations semiclassical method recently developed by us has shown with only six ab initio trajectories to evaluate eigenvalues and eigenfunctions at the accuracy level of thousands trajectory semiclassical initial value representation simulations.     

First principles calculation of the thermodynamic properties of silicon clusters

The thermodynamic properties of Si clusters are calculated using first principles quantum methods combined with molecular dynamics for simulating the trajectories of clusters. A plane wave basis is used with ab initio pseudo potentials and the local density approximation for determining the electronic energies and forces. Langevin molecular dynamics simulates thermal contact with a constant temperature reservoir. Vibrational spectra, moments of inertia, anharmonic corrections, and free energies are predicted for Si₂ through Si₅. The translational contribution is based on the ideal gas limit. The rotation contribution is approximated using a classical rigid rotator. Vibrational modes are determined from the dynamical matrix in the harmonic approximation. Corrections due to anharmonicity and coupling between rotational and vibrational modes are fit from the molecular dynamics simulations. Received: 17 September 1997 / Accepted: 14 October 1997     

First principles investigation of chromium carbide, CrC

We have investigated the electronic structure of 14 states of the experimentally unknown diatomic molecule chromium carbide, CrC, using standard multireference configuration interaction methods and high quality basis sets. We report potential curves, binding energies, and a number of spectroscopic parameters. The ground state of CrC, X 3Sigma-, displays triple-bond character with a binding energy of D(e)=89 kcal/mol and an internuclear separation of r(e)=1.63 A. The first excited state (1 5Sigma-) lies 9.2 kcal/mol higher. All the states studied are fairly ionic, featuring an electron transfer of 0.3-0.5e- from the metal atom to the carbon atom.     

First example of a covalently bound dimeric inverted porphyrin

Reaction of 5,10,15,20-tetraphenyl-2-aza-21-carbaporphyrinatonickel(II) with dihalomethanes in the presence of a proton scavenger gives a 2,21'-CH2-linked dimer of Ni(II) inverted porphyrins with the yield reaching 90% and its 2,2'-linked isomer as a minor product.     

First principles studies on boron sites in zeolites

A systematic computational investigation on protonated and nonprotonated boron-containing zeolites (boralites), performed by using different periodic density functional theory approximations, is presented. Both minimum energy structures and finite temperature behavior of model boron sodalites were analyzed. All of the adopted computational schemes agree in predicting an acid site composed of a silanol Si-OH group loosely linked to a planar BO(3) structure in the protonated system and a BO(4) tetrahedral site in the sodium-containing zeolite. Calculated structural and vibrational properties are in line with experimental data. Comparisons of the protonated boralite site with Al and Ga zeolitic acid sites are discussed as well. Results indicate that this class of mild acid catalysts is characterized by significant framework flexibility and pronounced thermal effects due to the loosely bound acid site.     

First principles predictions of thermophysical properties of refrigerant mixtures

We present pair potentials for fluorinated methanes and their dimers with CO(2) based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures with CO(2) without adjustment. Ab initio calculations on trimers are used to model the effects of nonadditive dispersion and induction. Simulations using these potentials reproduce the experimental phase-coexistence properties of CH(3)F within 10% over a wide range of temperatures. The phase coexistence curve of the mixture of CH(2)F(2) and CO(2) is reproduced with an error in the mole fractions of both phases of less than 0.1. The potentials described here are based entirely on ab initio calculations, with no empirical fits to improve the agreement with experiment.     

First principles study of photostability within hydrogen-bonded amino acids

The photochemistry and photophysics of a two-glycine minimal model is studied at the CASPT2//CASSCF level of theory. Different photoinduced processes are discussed, on the basis of the calculated minimum energy paths and the characterization of the electronic state crossings. Two main processes could provide UV-photostability to the hydrogen-bonded peptide system: (i) forward-backward photoinduced electron/proton transfer involving the H in the hydrogen bond, (ii) singlet-singlet energy transfer between two amino acids, providing ultrafast population of the low-energy n,π* state.     

First principles calculation of the mechanical compression of two organic molecular crystals

The mechanical compression curves for the organic molecular crystals 1,1-diamino-2,2-dinitroethylene and beta-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (beta-HMX) are calculated using the Hartree-Fock approximation to the solutions of the many-body Schr?dinger equation for a periodic system as implemented in the computer program CRYSTAL. No correction was made for basis set superposition error. The equilibrium lattice parameters are reproduced to within 1% of reported experimental values. Pressure values on the isotherm also agree well with reported experimental values. To obtain accurate results, the relaxation of all the atomic coordinates as well as the lattice parameters under a fixed volume constraint was required.     

Immunological determination of triazine pesticides bound to soil humic acids (bound residues)

An immunological method for the determination of triazine herbicides covalently bound to soil humic acids has been developed. A sandwich-immunoassay has been performed, based on both polyclonal humic acid-antibodies and monoclonal triazineantibodies. A peroxidase-labelled third antibody has been used for the photometric detection. A triazine-humic acid conjugate served as calibration standard. The coupling density for this conjugate has been determined by measuring the difference of free amino groups both with ninhydrin and with the trinitrobenzene sulfonic acid method. In addition, the coupling density has been confirmed by scintillation counting using a ¹⁴C-atrazine derivative. Due to nonspecific interactions between antibody proteins and humic acids, different blocking steps had to be performed. Finally, the assay has been applied to a triazine contaminated soil sample. Humic acids (including bound residues) have been extracted by diluted sodium carbonate solution. Concentrations of bound atrazine residues have been found in the range of 2 mg/kg soil on fields where triazine herbicides has been applied over a period of 21 years. These results are comparable to both the applied amount and the nonextractable fraction.     

Immunological determination of triazine pesticides bound to soil humic acids (bound residues)

An immunological method for the determination of triazine herbicides covalently bound to soil humic acids has been developed. A sandwich-immunoassay has been performed, based on both polyclonal humic acid-antibodies and monoclonal triazineantibodies. A peroxidase-labelled third antibody has been used for the photometric detection. A triazine-humic acid conjugate served as calibration standard. The coupling density for this conjugate has been determined by measuring the difference of free amino groups both with ninhydrin and with the trinitrobenzene sulfonic acid method. In addition, the coupling density has been confirmed by scintillation counting using a (14)C-atrazine derivative. Due to nonspecific interactions between antibody proteins and humic acids, different blocking steps had to be performed. Finally, the assay has been applied to a triazine contaminated soil sample. Humic acids (including bound residues) have been extracted by diluted sodium carbonate solution. Concentrations of bound atrazine residues have been found in the range of 2 mg/kg soil on fields where triazine herbicides has been applied over a period of 21 years. These results are comparable to both the applied amount and the nonextractable fraction.     

First principles studies of thermal decomposition of anhydrous zinc oxalate

The highly reactive and unstable exothermal features of methyl ethyl ketone peroxide (MEKPO) have led to a large number of thermal explosions and runaway reaction accidents in the manufacturing process. To evaluate the self-accelerating decomposition temperature (SADT) of MEKPO in various storage vessels, we used differential scanning calorimetry (DSC) and vent sizing package 2 (VSP2). The thermokinetic parameters were, in turn, used to calculate the SADT from theoretical equations based on the Semenov model. This study aimed at the SADT prediction value of various storage vessels in Taiwan compared with the UN 25 kg package and UN 0.51 L Dewar vessel. An important index, such as SADT, temperature of no return (T _NR) and adiabatic time maximum rate (TMR_ad), was necessary and useful to ensure safe storage or transportation for self-reactive substances in the process industries.     

First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

First principles molecular dynamics study of filled ice hydrogen hydrate

We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C(2) by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and∕or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and∕or low temperatures.     

First principles simulations of the electrochemical lithiation and delithiation of faceted crystalline silicon

Silicon is of significant interest as a next-generation anode material for lithium-ion batteries due to its extremely high capacity. The reaction of lithium with crystalline silicon is known to present a rich range of phenomena, including electrochemical solid state amorphization, crystallization at full lithiation of a Li(15)Si(4) phase, hysteresis in the first lithiation-delithiation cycle, and highly anisotropic lithiation in crystalline samples. Very little is known about these processes at an atomistic level, however. To provide fundamental insights into these issues, we develop and apply a first principles, history-dependent, lithium insertion and removal algorithm to model the process of lithiation and subsequent delithiation of crystalline Si. The simulations give a realistic atomistic picture of lithiation demonstrating, for the first time, the amorphization process and hinting at the formation of the Li(15)Si(4) phase. Voltages obtained from the simulations show that lithiation of the (110) surface is thermodynamically more favorable than lithiation of the (100) or (111) surfaces, providing an explanation for the drastic lithiation anisotropy seen in experiments on Si micro- and nanostructures. Analysis of the delithiation and relithiation processes also provides insights into the underlying physics of the lithiation-delithiation hysteresis, thus providing firm conceptual foundations for future design of improved Si-based anodes for Li ion battery applications.     

First principles calculation of the optical properties and stability of hydrogenated silicon clusters

Optical properties and stability of hydrogenated silicon clusters are investigated using density functional pseudopotential calculation. The dipole transitions between the band-edge orbitals are allowed, in contrast to the indirect gap in bulk silicon. Evolution of a small amount of hydrogen atoms enhances the dipole transition, increasing the photoluminescence intensity. Further dehydrogenation creates gap states due to dangling bonds, which may decrease the photoluminescence intensity via nonradiative recombination processes. The Stokes shift is also estimated by calculating the relaxed structure of the excited state within the local density approximation. © 1994 John Wiley & Sons, Inc.     

First principles study of the carbon-(silicon-) doped La13 clusters

The structural stability and physical properties have been studied for carbon-(silicon-) doped La(13) clusters using DMOL method based on density-functional theory. Doped La(13) clusters prefer to be icosahedron. Substitutional doping with a carbon or silicon impurity makes some clusters closed electronic shell, especially in icosahedral isomers. Substitutional doping of icosahedral La(13) clusters is found to be favorable at surface sites of clusters, especially for Si-doped La(13) cluster, which is very likely to be formed during the doping process. In addition, the structural distortions due to the doping are discussed.     

NMR determination of the bioactive conformation of peloruside A bound to microtubules

We report here on the determination of the conformation of Peloruside A bound to biochemically stabilized microtubules, by using TR-NOESY NMR experiments. As a previous step, the conformation of the free molecule in water solution has also been deduced. Despite the large size of the ring, Peloruside A mainly adopts two conformations in water solution. A conformational selection process takes place, and the microtubules-bound conformer is one of those present in the water solution, different than that existing in chloroform medium. A model of the binding mode to tubulin has also been proposed, by docking the bioactive conformation of peloruside, which involves the alpha-tubulin monomer, in contrast with taxol, which binds to the beta-monomer.