In-plane structure and ordering at liquid sodium surfaces and interfaces from ab initio molecular dynamics

Atoms at liquid metal surfaces are known to form layers parallel to the surface. We analyze the two-dimensional arrangement of atoms within such layers at the surface of liquid sodium using ab initio molecular dynamics (MD) simulations based on a full version of density functional theory. Nearest neighbor distributions at the surface indicate mostly fivefold coordination, though there are noticeable fractions of fourfold and sixfold coordinated atoms. Bond angle distributions suggest a movement toward the angles corresponding to a sixfold coordinated hexagonal arrangement of the atoms as the temperature is decreased towards the solidification point. We rationalize these results with a distorted hexagonal model at the surface, showing a mixture of regions of five- and sixfold coordination. The liquid surface results are compared with classical MD simulations of the liquid surface, with similar effects appearing, and with ab initio MD simulations for a model solid-liquid interface, where a pronounced shift towards hexagonal ordering is observed as the temperature is lowered.     

Ab initio studies of

Ab initio calculations of the [1,5]-H shift in (3Z)-penta-1,3-diene and other substituted pentadienes and heteroanalogues using the hybrid density functional Becke3LYP with the 6-31G basis set are presented. Electron-donating substituents, such as methoxy in (3Z)-3-methoxypenta-1,3-diene 1, or heteroatoms such as a nitrogen atom in (Z)-ethylidenevinylamine 2, (1Z)-buta-1,3-dienylamine 3, (2Z)-but-2-enylideneamine 4, (Z)-allylidenemethylamine 5, and methylene-(Z)-propenylamine 6 are introduced. The electron-withdrawing fluoride is substituted for the hydrogen atoms in (3Z)-3-fluoropenta-1,3-diene 7, (3Z)-2,4-difluoropenta-1,3-diene 8, (3Z)-1,1',2,3,4,5,5'-heptafluoropenta- 1,3-diene 10, (1E,3E)-1,3,5-trifluoropenta-1,3-diene 11, and (1Z,3E)-1,3,5- trifluoropenta-1,3-diene 13. A detailed analysis of the geometries, energies, and electronic characteristics of the sigmatropic transposition compared to those of the unsubstituted case provides insights into substituent effects of this prototype of pericyclic reaction. The inductive and mesomeric effects of heteroatoms or heterosubstituents are of a great importance and in a continuous balance in the energetics of the transformation. Sterics can also play an important role due to the geometrical constraints of the reaction. As a general trend, decreasing the electron density of the phi system destabilizes the aromatic transition structure and increases the activation energy, and vice versa.     

Ab initio studies of a water layer at transition metal surfaces

This paper presents a detailed study of a water adlayer adsorbed on Pt(111) and Rh(111) surfaces using periodic density functional theory methods. The interaction between the metal surface and the water molecules is assessed from molecular dynamics simulation data and single point electronic structure calculations of selected configurations. It is argued that the electron bands around the Fermi level of the metal substrate extend over the water adlayer. As a consequence in the presence of the water layer the surface as a whole still maintains its metallic conductivity-a result of a crucial importance for understanding the process of electron transfer through the water/metal interface and electrochemical reactions in particular. Our results also indicate that there exists a weak bond between the hydrogen of the water and the Rh metal atoms as opposed to the widespread (classical) models based on purely repulsive interaction. This suggests that the commonly used classical interactions potentials adopted for large scale molecular dynamics simulations of water/metal interfaces may need revision. Two adsorption models of water on transition metals with the OH bonds pointing towards or away of the surface are also examined. It is shown that due to the very close values of their adsorption energies one should consider the real structure of water on the surface as a mixture of these simple "up" and "down" models. A model for the structure of the adsorbed water layer on Rh(111) is proposed in terms of statistical averages from molecular dynamics simulations.     

Ab initio studies on calicene

Optimum geometries of planar and 90°-twisted C_2v calicene are calculated with single-configuration STO-3G and 3-21-G wavefunctions. The barrier to ring–ring rotation is computed. Bond alternation is pronounced in the planar form and decreases in the twisted form, while dipolar character increases on twisting.     

Ab initio methods for reactive potential surfaces

Case studies of ten reactions using a variety of standard electronic structure methods are presented. These case studies are used to illustrate the usefulness and shortcomings of these standard methods for various classes of reactions. Limited comparisons with experiment are made. The reactions studied include four radical-radical combinations, H + CH(3)--> CH(4), CH(3) + CH(3)--> C(2)H(6), H + HCO --> H(2)CO and CH(3) + HCO --> CH(3)CHO, three abstraction reactions, H + HO(2)--> H(2) + O(2), H + HCO --> H(2) + CO and CH(3) + HCO --> CH(4) + CO, a radical-molecule addition, H + HCCH --> C(2)H(3), and two molecular decompositions, H(2)CO --> H(2) + CO and CH(3)CHO --> CH(4) + CO. The electronic structure methods used are DFT, MP2, CCSD(T), QCISD(T), CASSCF, CASPT2, and CAS+1+2+QC.     

Ab initio studies of arginine and deaminoarginine

L-Arginine and Deaminoarginine were studied via quantum chemical ab initio calculations using the STO -3G basis set for arginine and the STO -3G and 3–21G basis sets for deaminoarginine. It was found that the most stable conformations are the ones featuring the carboxyl group slightly twisted versus the rest of the molecule, which adopts an extended conformation. It was also found that the cyclic zwitterion is less stable than the neutral cyclic conformation and that there is a barrier to the proton transfer from the carboxyl's oxygen to one of guanidine moiety's nitrogens.     

Ab initio molecular-dynamics study of liquid formamide

Properties of neat liquid formamide (HCONH2) have been studied by the combination of gradient-corrected density-functional theory, norm-conserving pseudopotentials, and the adaptive finite-element method. The structural and dynamical quantities have been calculated through molecular dynamics simulations under the Born-Oppenheimer approximation. Satisfactory agreement with experimental data was obtained for both intramolecular and intermolecular properties. Our results are also compared with those of the empirical potential functions to clarify their accuracies.     

Ab initio studies of methylenecarbene and isoelectronic species

Optimum equilibrium geometries, energetics, harmonic vibrational frequencies, and infared intensities within the double harmonic approximation are computed for methylenecarbene, CCH₂, and isoelectronic species involving silicon and germanium at both the SCF level of theory and the level of second-order perturbation theory using a 6-311G(2df, 2p) basis set or its equivalent. Optimum equilibrium geometries and energetics are also computed at both levels of theory using a smaller 6-311G(d, p) basis set or its equivalent. This investigation of these species is the first to include all of the systems with germanium. In addition, this present work is the first study to includef-type polarization functions in a systematic investigation of the molecular structure and properties of all the molecules in the series. Acetylenic structures are also computed for energy comparisons. Of all the linear isomers, only acetylene is found to be a minimum on the potential energy surface. However, all of the C_2v structures are found to be local minima. Both the C_2v and linear structures will serve as a basis for future work involving mapping the entire hyperenergy surfaces of all of the molecular systems in the series.     

Ab initio studies of small AlmFen clusters

The equilibrium geometrical structures of small Al_mFe_n clusters have been determined through ab initio calculation of the cluster total energy at the UB3LYP/Lanl2dz level. For dimers of iron and aluminum, the dissociation energies, the equilibrium atomic distances, and the vibrational frequencies were calculated. The agreement between calculations and experiments is reasonable. The ground stable geometrical structures of Fe₄, FeAl₃, Fe₃Al and Fe₂Al₂ clusters favor three-dimension configurations, but Al₄ tetramers are planar structures. The Al-rich tetramers are more stable than the other two composition tetramers. This is different from that of bulk alloys.     

Ab initio studies of peroxynitrite anion-water complexes

Quantum mechanical methods have been applied to thecis-ONOO^–-H₂O,cis-ONOO^–-(H₂O)₂ andtrans- ONOO^–-H₂O complexes. Equilibrium geometries, binding energies, net atomic charges and vibrational frequencies are presented for several different arrangements. The MØller-Plessett second-order perturbation (MP2) method predicted shorter hydrogen bonds than the SCF method, but the computed Hartree-Fock (HF) binding energies are similar to counterpoise corrected MP2 values. The geometry changes of ONOO^– and water after solvation are examined. The ONOO^– and H₂O bond length changes follow typical hydrogen bond structural trends, whereas bond angles in ONOO^– are unaffected when the hydrogen bond is formed, similar to the conclusions from NO ₂ ^– -(H₂O) _n HF/6-31G studies and Monte Carlo simulations. Thecis-ONOO^–-(H₂O) _n frequencies are compared with the solution Raman spectrum and with calculations on isolated ONOO^–.     

Ab initio studies of benzocyclopropenone, benzocyclopropenone-containing

Ab initio calculations were carried out on cyclopropenone, 1, benzocyclopropenone, 2, the benzocyclopropenone-containing [2.2]paracyclophane derivative tetracyclo[8.3.2.(4,7)O(11,13)]heptadeca-1(13),4,6,10,14,16-hexaen-12-one, 3, its decarbonylation product tricyclo[8.2.2.2(4,7)]hexadeca-1(12), 4,6,10,13-pentaen-15-yne, 5, a benzyne intermediate, and the bridged benzobarrelene derivative, pentacyclo[5.5.2.2.(1,4)O(4,14)O(10,13)]hexadeca-2,7,9,13,15-pentaene, 6. These calculations suggest that benzocyclopropenone-containing [2.2]paracyclophane, 3, and highly strained bridged benzobarrelene, 6, could exist as stable species. Both aryl rings of the benzocyclopropenone derivative 3 are predicted to be distorted from planarity. This distortion relieves some angle strain present in planar benzocyclopropenone due to the presence of the annulated three-membered ring. Calculations on benzobarrelene, 8, and [2.2]paracyclophane, 4, were performed for comparison to gain a better understanding of the strain borne in bridged benzobarrelene 6. The activation barrier for the intramolecular [4 + 2] cycloaddition of 5 to give 6 was estimated at 18.8 kcal/mol while that for the corresponding [2 + 2] cycloaddition, giving the less stable 9, was 54.5 kcal/mol. The [2 + 2] cycloaddition's transition state was twisted in a manner reminiscent of the conservation of orbital symmetry prediction for an unstrained system.     

Ab initio computed diabatic potential energy surfaces of OH-HCl

The two four-dimensional diabatic potential energy surfaces (DPESs) for OH-HCl are computed that correlate with the twofold degenerate (2)Pi ground state of the free OH radical. About 20 000 points on the surface are obtained by the ab initio coupled-cluster and multi-reference configuration interaction methods. Analytic forms for the diabatic potential energy surfaces are derived as expansions in complete sets of orthogonal functions depending on the three intermolecular angles. The numeric computation of the angular expansion coefficients is discussed. The distance-dependence of the angular coefficients is represented by the reproducing kernel Hilbert space method. It is checked that both diabatic potentials converge for large intermolecular separations to the values computed directly from the electrostatic multipole expansion. The final DPESs are discussed and illustrated by some physically meaningful one- and two-dimensional cuts through them.     

X-ray scattering studies of surfaces and interfaces

Here we shall briefly review the basics and some applications of x-ray specular reflectivity and diffuse scattering techniques. These x-ray scattering techniques are uniquely suited to study of the structure of surfaces and interfaces at atomic resolutions as they are nondestructive and can probe even interfaces which are buried. The study of structure of surfaces and interfaces is not only required in understanding physics in reduced dimensions but is also essential in developing technologically important materials.     

Ab initio molecular orbital studies of polyethylene deformation

A molecular LCAO Hartree-Fock procedure was used to calculate total energies of axially stretched normal paraffins containing up to nine carbon atoms. The results are used to model the mechanical properties of polyethylene.     

Ab initio studies on the thermolysis of azetidine

The reaction mechanism of the thermolysis of azetidine to form ethylene and methylen-imine has been studied by ab initio SCF MO method at STO--3G and 3-21G levels. Two possible step-wise pathways are explored. One is the breaking of C--C bond as the first step, while the other is thebreaking of C--N bond. All the stationary points on the potential energy surface (PES) are fully optimiz-ed. MP2 / 3-21G single point calculations on all stationary points and MCSCF / STO-3G computationsfor some stationary points are also carried out. The calculations indicate that azetidine decomposesvia biradicaloid intermediates and the cleavage of C--N bond is preferable to that of C--C bond.     

Ab initio molecular dynamics of liquid 1,3-dimethylimidazolium chloride

Density-functional-based Car-Parrinello molecular dynamics (CPMD) simulations have been performed for the ionic liquid 1,3-dimethylimidazolium chloride, [dmim]Cl, at 438 K. The local structure of the liquid is described in terms of various partial radial distribution functions and anisotropic spatial distributions, which reveal a significant extent of hydrogen bonding. The cation-anion distribution simulated with the BP86 functional is in qualitative agreement with the structural model derived from neutron diffraction data for the liquid, whereas the theoretical cation-cation distribution shows less satisfactory accord. Population analyses indicate noticeable charge transfer from anions to cations, and specific CH...Cl hydrogen bonds are characterized in terms of donor-acceptor interactions between lone pairs on Cl and antibonding sigma(CH) orbitals.     

Ab initio effective core potential studies on polymers

Ab initio crystal orbital calculation with the effective core potential (ECP) approximation is performed on infinite poly-yne, all-trans-polyethylene, and all-trans-polysilane. The optimized bond lengths of poly-yne are predicted to be 1.130 Å and 1.321 Å with the split valence LP-31G basis set and agree fairly well with 4-31G results, 1.166 Å and 1.339 Å. The energy band structures of poly-yne and all-trans-polyethylene obtained from ECP calculations are in reasonable agreement with those from the all electron calculations. The fully optimized geometries of all-trans-polysilane are also predicted with the LP-31G basis set asr _SiSi = 2.264 Å,r _SiH = 1.493 Å, \(\sphericalangle\) SiSiSi = 118.97 °, and \(\sphericalangle\) HSiH = 100.35 °. The computational time for calculations of polysilane is found roughly to be comparative to that of polyethylene under ECP approximations.     

Ab initio studies of properties of small potassium clusters

We have studied the properties of various isomers of potassium clusters containing even number of atoms ranging from 2 to 20 at the ab initio level. The geometry optimization calculations of the isomers of each cluster are performed by using all-electron density functional theory with gradient corrected exchange-correlation functional. Using the optimized geometries of different isomers we investigate the evolution of binding energy, ionization potential, and static polarizability with the increasing size of the clusters. The polarizabilities are calculated by employing M?ller-Plesset perturbation theory and time-dependent density functional theory. The polarizabilities of dimer and tetramer are also calculated by employing large basis set coupled cluster theory with single and double excitations and perturbative triple excitations. The time-dependent density functional theory calculations of polarizabilities are carried out with two different exchange-correlation potentials: (i) an asymptotically correct model potential and (ii) within the local density approximation. A systematic comparison with the other available theoretical and experimental data for various properties of small potassium clusters mentioned above has been performed. These comparisons reveal that both the binding energy and the ionization potential obtained with gradient-corrected potential match quite well with the already published data. Similarly, the polarizabilities obtained with M?ller-Plesset perturbation theory and with model potential are quite close to each other and also close to experimental data.