Ab Initio Molecular Calculations Research Articles

Ab initio density functional theory applied to the structure and proton dynamics of clays

Ab initio molecular dynamics and total energy calculations are combined to determine the orientation of hydroxyl groups and to localize the components of the vibrational spectra of dickite. The inner hydroxyl and one inner-surface hydroxyl form a horizontally oriented pair producing high-frequency components in the region of the O–H stretching. Other two hydroxyls make interlayer contacts and produce two down-shifted stretching bands.

Relativistic pseudopotentional incorporating core/valence polarization and nonlocal effects.

A relativistic pseudopotentional (RPP) for use in ab initio molecular electronic structure calculations is derived in the context of the relativistic effective core potential (REP) method of Lee et al. The resulting atom-specific RPP has salient features of the REP imbedded within it while retaining the form of a functional that is dynamically defined at runtime when used in calculations on molecules. The RPP is determined from Dirac-Fock wave functions for the isolated atom. Outer core two-electron interactions are incorporated into the RPP by means of variable coefficients that are defined in the context of the final molecular wave function. This form permits polarization of the outer core shells analogous to that occurring in all-electron molecular Hartree-Fock calculations while retaining these shells as part of the atomic pseudopotentional. Use of the RPP in post-Hartree-Fock molecular calculations permits the incorporation of core/valence correlation effects.

Effective Group Potentials. 1. Method

In the first paper of this series, we will describe a method, called effective group potentials (EGP), aimed at simplifying molecular ab initio calculations for large systems involving bulky ligands as long as these ligands can be supposed to play the role of spectator groups. This method should be applicable to all types of bondings between active and the spectator parts. The different steps used in the definition of the EGP are closely related to those used for atomic effective core potentials (ECP) which are commonly used with great success in ab initio calculations involving heavy atoms.

The HD and HD̄ Methods for Accelerating the Convergence of Three-Center Nuclear Attraction and Four-Center Two-Electron Coulomb Integrals over B Functions and Their Convergence Properties

Three-center nuclear attraction and four-center two-electron Coulomb integrals over Slater-type orbitals are required for ab initio and density functional theory (DFT) molecular structure calculations. They occur in many millions of terms, even for small molecules and require rapid and accurate evaluation. The B functions are used as a basis set of atomic orbitals. These functions are well adapted to the Fourier transform method that allowed analytical expressions for the integrals of interest to be developed. Rapid and accurate evaluation of these analytical expressions is now made possible by applying the HD and HD̄ methods for accelerating the convergence of the semi-infinite oscillatory integrals. The convergence properties of the new methods are analysed. The numerical results section shows the high predetermined accuracy and the substantial gain in the calculation times obtained using the new methods.

Efficient syntheses and ring-opening reactions of trans- and cis-oxazoline-5-carboxylates

[formula: see text] cis- and trans-Oxazoline-5-carboxylates were synthesized efficiently from isopropyl trans-cinnamate utilizing the Sharpless AA reaction. trans-Oxazoline was much more reactive than the cis-isomer toward ring opening reactions. From ab initio molecular calculations, the cis-isomer was predicted to be less reactive than the trans-isomer by 2.7 kcal/mol. Both syn and anti acetylthio esters and anti diamino esters were synthesized from these cis- and trans-oxazoline-5-carboxylates.

Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase:ab initio and SIBFA molecular mechanics calculations

The interaction of Zn2+ with glycine (Gly) in the gas phase is studied by a combination of ab initio and molecular mechanics techniques. The structures and energetics of the various isomers of the Gly–Zn2+ complex are first established via high-level ab initio calculations. Two low-energy isomers are characterized: one in which the metal ion interacts with the carboxylate end of zwitterionic glycine, and another in which it chelates the amino nitrogen and the carbonyl oygen of neutral glycine. These calculations lead to the first accurate value of the gas-phase affinity of glycine for Zn2+. Ab initio calculations were also used to evaluate the performance of various implementations of the SIBFA force field. To assess the extent of transferability of the distributed multipoles and polarizabilities used in the SIBFA computations, two approaches are followed. In the first, approach (a), these quantities are extracted from the ab initio Hartree–Fock wave functions of glycine or its zwitterion in its entirety, and for each individual Zn2+-binding conformation. In the second, approach (b), they are assembled from the appropriate constitutive fragments, namely methylamine and formic acid for neutral glycine, and protonated methylamine and formate for the zwitterion; they undergo the appropriate vector or matrix rotation to be assembled in the conformation studied. The values of the Zn2+–glycine interaction energies are compared to those resulting from ab initio SCF and MP2 computations using both the all-electron 6-311+G(2d,2p) basis set and an effective core potential together with the valence CEP 4-31G(2d) basis set. Approach (a) values closely reproduce the ab initio ones, both in terms of the total interaction energies and of the individual components. Approach (b) can provide a similar match to ab initio interaction energies as does approach (a), provided that the two constitutive Gly building blocks are considered as separate entities having mutual interactions that are computed simultaneously with those occurring with Zn2+. Thus, the supermolecule is treated as a three-body rather than a two-body system. These results indicate that the current implementation of the SIBFA force field should be adequate to undertake accurate studies on zinc metallopeptides. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 963–973, 2000

Theoretical study of the(3×2)reconstruction ofβ-SiC(001)

By means of ab initio molecular dynamics and band structure calculations, as well as using calculated STM images, we have singled out one structural model for the (3x2) reconstruction of the Si-terminated (001) surface of cubic SiC, amongst several proposed in the literature. This is an alternate dimer-row model, with an excess Si coverage of 1/3, yielding STM images in good accord with recent measurements [F.Semond et al. Phys. Rev. Lett. 77, 2013 (1996)].

Analysis of a nonlinear optical response of CN− ions adsorbed on metal electrode: tentative interpretation by means of ab initio molecular calculations

Abstract The electronic and vibrational properties of CN − adsorbed on M metals (M=Pt, Ag, Au) have been studied through different quantum calculations (SCF, MCSCF and DFT) of the MCN − and MNC − molecular ions; moreover the IR and Raman intensities have been computed for each vibrational frequency. All these theoretical results allow us to have a better understanding of the spectra obtained by SFG (or DFG) experiments on Pt, Ag and Au electrodes which exhibit two resonances with Pt and an unique one with Ag and Au.

Bioisosteric Approach In The Design of New Dopaminergic/ Serotonergic Ligands

Dopaminergic and serotonergic ligands are widely applied in the therapy of some severe diseases in humans connected to the malfunctioning of the corresponding membrane receptors within the CNS. However, no pharmaceuticals of this type with an ideal therapeutic index have been synthesized so far and there is a constant need of producing new dopaminergic/serotonergic ligands with improved properties especially with regard to undesirable side effects expressed after a prolonged therapy. Dopaminergic/serotonergic ratio turned out to be important for a fine tuning of pharmacological profile of new ligands. Employing a bioisosteric approach, we have synthesized numerous quinoxalinediones, benztriazoles, benzimidazoles and 2-substituted benzimidazoles as potential dopaminergic and/or mixed dopaminergic/serotonergic compounds. With this purpose, benzimidazole and its derivatives were incorporated into phenylethylamine, 3- and 4-substituted phenylethylpiperidine, 1-substituted 4-arylpiperazine and semirigid 2-aminotetralin frame and the resulting ligands were checked for the binding affinity at the D1 and D2 dopamine and 5-HT1A serotonin receptors in radioligand binding assays in vitro. Synaptosomal membranes prepared from bovine caudate nuclei and hippocampi served as a source of the dopamine and serotonin receptors, respectively. [3H]SCH 23390 (D1 receptor-selective), [3H]spiperone (D2 receptor-selective) and 8 OH [3H]DPAT (5-HT1A receptor-selective) were employed as radioligands in competition binding assays. Properties of substituents introduced into position 2 of benzimidazole ring, as well as the nature of the frame into which benzimidazole pharmacophore was incorporated have been shown to determine ligand binding affinity, mode of action and receptor preference, i.e. dopaminergic/serotonergic affinity ratio. Benzimidazolyl-2-thione and benztriazole derivatives were the most potent dopaminergic/serotonergic ligands. Molecular ab initio calculations of the electronic properties of pharmacophoric entities of the new ligands revealed different electron density distribution around the benzene ring in the active and inactive ligands. It can be assumed that this difference influences the properties of pi-pi interactions in a receptor-ligand complex. The results are discussed in comparison with the data of other authors working on similar topics.

Efficient evaluation of Coulomb integrals: the nonlinearD- and -transformations

The two-electron multicentre Coulomb integrals constitute the rate-limiting step of ab initio and density functional theory (DFT) molecular structure calculations. Speed-up can be achieved by limiting the number of integrals to evaluate analytically but these analytical evaluations remain rate-limiting for large molecules. Here we apply the nonlinear D- and -transformations to evaluate Coulomb integrals over B-functions more rapidly than the alternative transformation methods to a given predetermined high accuracy.

Study of the OH- + CH2F2 Reaction by Selected Ion Flow Tube Experiments and ab Initio Calculations

The reaction OH- + CH2F2 → products has been investigated by both selected ion flow tube (SIFT) experiments and ab initio molecular calculations. The SIFT experiments showed that a bimolecular process, leading to two major anionic products, CHF2- (86%) and F- (11%), and one minor anionic product, HF2- (3%), is in competition with a three-body association leading to OH-·CH2F2 (where values in parentheses are the relative values of the detected anionic products at 300 K). From a pressure dependence study, an upper limit of the bimolecular reaction rate coefficient at 300 K is determined to be (2.4 ± 1.4) × 10-12 cm3 molecule-1 s-1. This shows a small negative temperature dependence, suggesting that the reaction proceeds via an ion-complex intermediate. These experimental results were rationalized using ab initio molecular orbital calculations. Stationary points on the reaction paths of the two main reaction channels were located at both the HF/6-31++G** and MP2/6-31++G** levels. The relative energies of the...

Potential role of silanones in the photoluminescence-excitation, visible-photoluminescence-emission, and infrared spectra of porous silicon

Ab initio molecular electronic structure calculations on select silanones, silylenes, and tricoordinated silicon compounds $\mathrm{Si}\mathrm{XYZ}$ with a dangling electron are presented. The calculations are used to evaluate the nature of the electronic spectra, which are to be associated with surface-bound Si/O/H compounds. In concert, they are used to suggest an explanation for the nature of the photoluminescence-excitation spectrum (PLE) and the subsequent visible luminescence (PL) from porous silicon (PS) based on the optical properties of the silanone-based oxyhydrides. In order to make this selection, we treat a set of compounds that includes the silanones ${\mathrm{Si}(\mathrm{O})\mathrm{H}}_{2},$ Si(O)H(OH), ${\mathrm{Si}(\mathrm{O})(\mathrm{OH})}_{2},$ ${\mathrm{Si}(\mathrm{O})\mathrm{H}(\mathrm{O}\mathrm{S}\mathrm{i}\mathrm{H}}_{3})$, ${\mathrm{Si}(\mathrm{O})\mathrm{H}(\mathrm{S}\mathrm{i}\mathrm{H}}_{3}),$ ${\mathrm{Si}(\mathrm{O})(\mathrm{OH})(\mathrm{S}\mathrm{i}\mathrm{H}}_{3}),$ ${\mathrm{Si}(\mathrm{O})(\mathrm{S}\mathrm{i}\mathrm{H}}_{3}{)}_{2},$ and ${\mathrm{Si}(\mathrm{O})(\mathrm{S}\mathrm{i}\mathrm{H}}_{3}{)(\mathrm{O}\mathrm{S}\mathrm{i}\mathrm{H}}_{3}),$ the silylenes HSiOH, HOSiOH, and ${\mathrm{HOSiOSiH}}_{3},$ and the tricoordinated silicon compounds ${\mathrm{SiH}}_{3},$ ${\mathrm{Si}(\mathrm{OH})\mathrm{H}}_{2},$ ${\mathrm{Si}(\mathrm{OH})}_{2}\mathrm{H},$ and ${\mathrm{Si}(\mathrm{OH})}_{3}.$ The silanone-based oxyhydride structures containing either an OH or ${\mathrm{OSiH}}_{3}$ group all display adiabatic ground-state singlet-excited-state triplet exciton separations in the range close to 400 nm. This adiabatic energy is consistent with the vertical transition energies associated with the PS excitation spectrum (PLE) as a large change in the $\mathrm{Si}\mathrm{=}\mathrm{O}$ bond distance $(\ensuremath{\sim}0.17\AA{})$ accompanies the transition from the silanone ground electronic singlet state to the low-lying triplet exciton (or its closely lying singlet coupled configuration). The maximum in the PLE spectrum, obtained through optical pumping from the lowest vibrational levels of the ground electronic state to considerably higher levels of the triplet exciton electronic state, should therefore be shifted to considerably shorter wavelength consistent with an absorption spectrum peaking at 350 nm as observed by several researchers. A shift to larger internuclear distance in the excited-state triplet exciton will also produce a considerable redshift in the PL emission spectrum relative to the absorption-excitation wavelengths, again consistent with experimental observation. The calculated IR spectra for the silanone-based oxyhydrides are also consistent with the observed Fourier transform IR spectra of porous silicon. In clear contrast, neither the silylenes nor the tricoordinated silicon compounds with dangling electrons can account for the excitation or emission features that are associated with PS as their lowest-lying transitions result in minimal changes in bonding and/or occur at much higher energy (shorter wavelength). The results obtained in this study also suggest that surface passivation or the saturation of valency is incommensurate with the formation of the fluorophors that will produce the emission from PS.

Structural comparison of 1β-Methylcarbapenem, Carbapenem and Penem: NMR studies and theoretical calculations

Structural comparisons of meropenem (1), desmethyl meropenem (2) and the penem analogue (3) which contain the same side chains at both C-2 and C-6 were performed using 1H NMR measurements together with 3-21G* level of ab initio MO and molecular mechanics calculations. The ab initio MO calculations reproduced the skeletons of these strained β-lactam rings in good agreement with the crystallographic data. 1H NMR measurements in aqueous solution together with molecular modeling studies indicated that there were conformational differences of the C-2 and C-6 side chains in this series of compounds. These observations suggested that the conformational differences could affect their biological activities.

A new petite list for post-SCF calculations

The Petite list ( Pl) algorithm is a well-known procedure for treating spatial symmetry in ab initio molecular calculations. In this methodology, all the redundancy due to spatial symmetry is eliminated and a unique list of elements is collected under the name of Pl. This list is processed as if there were no symmetry and the final quantity is then submitted to a symmetrization step. Dupuis and King proposed a Pl based on the procrastination of all except for the last batch of two-electron symmetry redundant integrals. This algorithm is of wide use, being extensively reported in the literature. Although this pl definition is well-suited to performing large scale Hartree-Fock calculations, this work points out the possibility of advantageous use of other Pl criteria in performing post-SCF calculations. This work proposes an original pl, and benchmarks are performed for SCF/MP2 calculations in water, benzene and hexafluoroethane with several basis sets. The computation time, memory requirements and general single-job performance are shown. The integral and SCF computer times are nearly doubled in CPU and elapsed time, but the transformation from atomic to molecular integral takes great advantage of the use of symmetry in all four steps. The timings for this transformation are rather favourable for the proposed Pl and work is in progress to extend this methodology to methods processing more extended transformations, as in CAS-SCF calculations.

Molecular charge density analysis

It is proposed to analyse the first-order reduced density matrix of a molecular wave function in terms of the first-order reduced density matrices of different states of the constituent atoms. With this an unambiguous partitioning of the molecular charge distribution in terms of the atomic charge distributions is obtained. Simple practical formulae are derived, such that in many ab initio molecular wave function calculations the analysis proposed can be carried out routinely. The results obtained should be useful for the interpretation of molecular wave functions in terms of their atomic constituents, as well as for the determination of atomic form factors to be used in X-ray molecular structure determination. Some simple examples are given, and the results obtained are compared with those obtained using other methods of analysis. Key words: charge density, density matrix, goodness-of-fit, correlation coefficient, standard deviation.

Elucidating the Origin of Conformational Energy Differences in Substituted 1,3-Dioxanes: A Combined Theoretical and Experimental Study.

13C NMR spectroscopy, ab initio quantum mechanics, and molecular mechanics have been used to investigate the trans-4-(trifluoromethyl)-2,2,6-trimethyl-1,3-dioxane chair/twist-boat equilibrium. The molecular mechanics calculations were based upon the MM3 and AMBER force fields. A 6-31G basis set was used for the ab initio calculations, and MP2 correlation corrections were applied. Both the ab initio and AMBER molecular mechanics calculations are consistent with the (13)C NMR chemical shift differences for the trans-4-(trifluoromethyl)-2,2,6-trimethyl-1,3-dioxane conformers. The predicted chair to twist-boat equilibrium suggested by the MM3 calculations is not consistent with the experimental data. These results support the suggestion by Howard et al. (Howard, A. E.; Cieplak, P.; Kollman, P. A. J. Comput.Chem. 1995, 16, 243-261) on the critical role of electrostatic interactions in determining the chair/twist-boat equilibrium.

Synthesis, electrochemistry and photoexcited-state properties of dinuclear ruthenium complexes bridged by 2,6′-bis(2-pyridyl)-2,2′:6,2″-thiazolo[4,5- d]-benzothiazole

The new bridging ligand, 2,6′-bis(2-pyridyl)-2,2′:6,2″-thiazolo[4,5- d]-benzothiazole (bptb) and its dinuclear Ru complexes have been synthesized. The combination of the transient absorption (TA) spectra and spectroelectrochemical difference spectra has led to the assignment of the lowest excited state for the dinuclear Ru(II) complexes as a Ru-to-bptb charge transfer state. Although the ab initio molecular calculations of bridging ligands have provided lower HOMO/LUMO energies for bptb compared to those of 2,6-bis(2-pyridyl)benzodiimidazole (dpimbH 2), the degree of electronic coupling for the dinuclear bptb complex is smaller than that for the dpimbH 2 complex from the analysis of intervalence charge transfer band. Since both dinuclear Ru complexes have a similar coordination environment, the Ru dπ-HOMO Lπ mixing is dominant for the metal-metal interaction through the hole transfer mechanism.

Ab initio studies on the mixed heterodimers of ammonia and hydrogen cyanide

Ab initio molecular structure calculations have been used to examine the association of NH 3 with HCN to form a heterodimer. Because of the potential importance of electron correlation in weakly associated complexes, the structure and energy of the heterodimers and the associated monomers are reported at both Hartree—Fock and Møller—Plesset levels of calculation. Other calculated properties including harmonic vibrational frequencies and rotational constants are also reported for each system. Several stationary points on the potential surface were located and characterized. In the two most stable configurations, the monomer units are associated through a hydrogen bond with HCN acting as the hydrogen donor. The structure predicted to be the most stable has a linear hydrogen bond and C 3v symmetry in accordance with the experimentally observed symmetric top spectrum. The stability of this structure is 5.28 kcal/mol (with MP2FULL/6-31 + G(3df, 2p) and 5.01 kcal/mol with counter-poise correction). The second structure having only C 1 symmetry is identified as a transition state. A third stable hydrogen bonded structure has HCN acting as the hydrogen acceptor and is the most weakly bound of the three.

Concerning the heats of formation of the [C, H 3, N] + [rad] radical cations

Ab initio molecular calculations carried out at the UQCISD(T)/6–311++G (3df, 2p) and RCCSD(T)/cc-pVTZ levels have been used to re-examine the heats of formation of the [C, H 3, N] + radical cations and related species. The following values have been obtained: Δ H 0 f,298 (H 2CNH) + =1046±10 kJ/mol, Δ H 0 f,298(HCNH 2) + =1030±10 kJ/mol, Δ H 0 f,298(HCNH 2)=236±10 kJ/mol, PA(H 2CNH)=864±10 kJ/mol, PA(HCNH 2)=1012±10 kJ/mol, IE a(H 2CNH)=9.9±0.2 eV and IE a(HCNH 2)=8.2±0.2 eV. Ionized aminocarbene (HCNH 2) + is definitely more stable than ionized methylenimine (H 2CNH) + .

Neutron Scattering Study of Vibrational Modes in Glassy Gel-xSnxSe2

ABSTRACTThe neutron vibrational density of states has been determined from neutron time-of-flight scattering in g-Ge1-xSnxSe2 with x = 0, 0.3, 0.35, and 0.5 to search for "floppy" modes. Previously Raman and Mossbauer studies1 have been interpreted on the basis that the addition of Sn to the GeSe2 network reduces the average number of mechanical constraints per atom allowing one to tune through the rigidity percolation threshold near x = 0.35. A comparison of the VDOS measured in this work below 10 meV for all samples shows that they are nearly identical indicating no evidence of the existence of floppy modes in these samples. Ab initio molecular dynamics2 calculations of the VDOS show good agreement with the measured results for g-GeSe2.