Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations

High level correlated quantum chemical calculations, using MP2 and local MP2 theory, have been performed for conformations of the disaccharide, beta-maltose, and the trisaccharide, 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose. For beta-maltose, MP2 and local MP2 calculations using the 6-311++G** basis set are in good agreement, predicting a global minimum gas-phase conformation with a counterclockwise hydrogen bond network and the experimentally-observed intersaccharide hydrogen bonding arrangement. For conformations of 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranose, MP2/6-311++G**, and local MP2/6-311++G** calculations do not provide a consensus prediction of relative energetics, with the MP2 method finding large differences in stability between extended and folded trisaccharide conformations. Local MP2 calculations, less susceptible to intramolecular basis set superposition errors, predict a narrower range of trisaccharide energetics, in line with estimates from Hartree-Fock theory and B3LYP and BP86 density functionals. All levels of theory predict compact, highly hydrogen-bonded conformations as lowest in energy on the in vacuo potential energy surface of the trisaccharide. These high level, correlated local MP2/6-311++G** calculations of di- and trisaccharide energetics constitute potential reference data in the development and testing of improved empirical and semiempirical potentials for modeling of carbohydrates in the condensed phase.     

DNA base trimers: empirical and quantum chemical ab initio calculations versus experiment in vacuo

A complete scan of the potential‐energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller–Plesset second‐order perturbation theory (RI‐MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T‐shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol^?1. The different behaviors of nonmethylated and methylated trimers is also discussed. The high‐level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple‐zeta basis set predicts 11 uracil trimer interaction energies with a root‐mean‐square error of 2.3 kcal mol^?1 relative to highly correlated ab initio theoretical calculations.     

Structure of isolated tryptophyl-glycine dipeptide and tryptophyl-glycyl-glycine tripeptide: ab initio SCC-DFTB-D molecular dynamics simulations and high-level correlated ab initio quantum chemical calculations

The tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides have been studied by means of molecular dynamic simulations combined with high-level correlated ab initio quantum chemical and statistical thermodynamic calculations. The lowest energy conformers were localized in the free energy surface. The structures of the different Trp-Gly and Trp-Gly-Gly conformers coexisting in the gas phase have been for the first time reported and their scaled theoretical IR spectra unambiguously assigned and compared with previous gas-phase experimental results. Common geometrical features have been systematically observed for the sequence Trp, Trp-Gly, and Trp-Gly-Gly. In addition, the peptide backbone of Trp-Gly-Gly has been compared with that of the previously studied Phe-Gly-Gly (Reha, D. et. al. Chem. Eur. J. 2005, 11, 6803). From the observed systematic structural behavior between these peptide analogues, it is expected that the gas-phase conformers of other similar aromatic small peptides would present equivalent geometries. The DFT methodology failed to describe the potential energy surface of the studied peptides since the London dispersion energy (not covered in DFT) plays a significant role in the stabilization of most stable conformers.     

MgH^+,Mg2H^+量子化学从头计算的研究

用量子化学自洽场分子轨道从头计算方法,采用STO-3G基组计算了MgH~+,Mg_2H~+离子的位能曲线与位能面;给出电子波函数与电子集居数;得到MgH~+的平衡构型键长γ_(Mg-H)1.60A.Mg_2H~+的平衡构型有C_(∞v)与D_(∞h)两类,前者为[Mg—Mg—H]~+,键长γ_(Mg-Mg)2.41,γ_(Mg-H)1.63A;后者为[Mg—H—Mg]~+,γ_(Mg-H)1.73A.前者的总能量比后者低50kcal/mol.还讨论了它们的稳定性.MgH~+的键长计算结果和实测值较吻合,Mg_2H~+的平衡构型计算结果支持了Porter从热力学研究提出的假设.     

Cluster models and ab initio calculations of (19)F NMR isotropic chemical shifts for inorganic fluorides

(19)F NMR isotropic chemical shift (delta(iso)) calculations are performed in crystallized compounds using the GIAO method with the B3LYP hybrid functional at DFT level. Clusters centered on the studied fluorine atoms mimic the crystalline structures. The 6-311+G(d) basis set is chosen for the central fluorine atom, and the LanL2DZ basis set for the others. The metal atoms are described by the 3-21G(2d) basis set or, when not available, by the CRENBL basis set with the corresponding ECP, and augmented with 2d polarization functions when existing. First, for high-symmetry systems (MF, MF(2), and MF(3) compounds), a systematization of the cluster building up from coordination spheres is proposed, generalized to fluoroperovskites and fluoroaluminates KAlF(4) and RbAlF(4). When applied to rather low symmetry systems such as barium fluorometalates BaMgF(4), BaZnF(4), and Ba(2)ZnF(6), the definition of the coordination spheres is far from easy. Then, for structures built up from a MF(6) octahedron network, we may define different "starting clusters": [FM(2)F(8)] for the shared fluorine atoms, [FMF(4)] for the unshared ones, and [FBa(4)](7+) for the "free" ones. Analogous "starting clusters" are then tested on compounds from the NaF-AlF(3), BaF(2)-AlF(3), and CaF(2)-AlF(3) binary systems and for alpha-BaCaAlF(7) that are also built up from a MF(6) octahedron network. For each of these corresponding fluorine sites, delta(iso) values are calculated with the "starting clusters" and several larger clusters and compared to the experimental delta(iso) values. For the barium-containing clusters, the RMS deviation is equal to 51 ppm. It is suggested that this result may be related to the poor quality of the barium basis sets for which no polarization functions are available for the moment. In total, chemical shifts were calculated for 122 fluorine sites, in a various range of compounds. For the clusters without barium, the ab initio method leads to a RMS equal to 22 ppm, which is a quite nice result keeping in mind that the (19)F chemical shift range is larger than 200 ppm.     

Set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data

A parametrization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e., vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl ether, sulfur dioxide, dimethyl sulfide, thiophene, hydrogen cyanide, acetonitrile, and nitromethane. Most of the models are able to describe the experimental VLE data with deviations of a few percent.     

Conformational stability of trivinylborane from vibrational spectra and ab initio calculations

The conformational stability, barriers to internal rotation and vibrational frequencies of trivinylborane have been determined from the vibrational spectra and ab initio calculations. The ab initio calculations have been carried out utilizing the RHF/3-21G, RHF/6-31G*, and MP2/6-31G* basis sets and support the vibrational data that there are two stable conformations in the fluid phases separated by a relatively small energy difference. One of the conformations is a near-planar form which has the three vinyl groups twisted out of the BC₃ plane and belongs to the C₃ point group. The other conformer has a non-planar structure and belongs to the C₁ point group. These and other calculated results are compared to the corresponding quantities obtained from the experiment.     

Understanding solvation in hydrofluoroalkanes: ab initio calculations and chemical force microscopy

Understanding solvation in hydrofluoroalkane (HFA) propellants is of great importance for the development of novel pressurized metered-dose inhaler (pMDI) formulations. HFA-based pMDIs are not only the most widely used inhalation therapy devices for treating lung diseases, but they also hold promise as vehicles for the systemic delivery of biomolecules to and through the lungs. In this work we propose a combined microscopic experimental and computational approach to quantitatively relate the chemistry of moieties to their HFA-philicity. Binding energy calculations are used to determine the degree of interaction between a propellant HFA and candidate fragments. We define a new quantity, the enhancement factor E, which also takes into account fragment-fragment interactions. This quantity is expected to correlate well with the solubility and the ability of the moieties of interest to impart stability to colloidal dispersions in HFAs. We use a methyl-based (CH) segment and its fluorinated analog (CF) to test our approach. CH is an important baseline case since it represents the tails of surfactants in FDA-approved pMDIs. CF was chosen due to the improved solubility and ability of this chemistry to stabilize aqueous dispersions in HFAs. Adhesion force from Chemical Force Microscopy (CFM) is used as an experimental analog to the binding energy calculations. The force of interaction between a chemically modified AFM tip and substrate is measured in a model HFA, which is a liquid at ambient conditions. Silanes with the same chemistry as the fragments used in the ab initio calculations allow for direct comparison between the two techniques. The CFM results provide an absolute scale for HFA-philicity. Single molecule (pair) forces calculated from the CFM experiments are shown to be in very good agreement to the E determined from the ab initio calculations. The ab initio calculations and CFM are corroborated by previous experimental studies where propellants HFAs are seen to better solvate the CF functionality.     

Conformational analysis of N-methylglycine and N,N-dimethylglycine by ab initio calculations

Eight of the most stable conformers of N-methylglycine (NMG) and five of N,N-dimethylglycine (DMG) were analyzed by high level ab initio calculations. Since NMG has only one amino hydrogen and a carboxylic acid hydrogen, it is capable of the formation of various types of hydrogen-bonded conformers and as a result is ideally suited to studying the importance of hydrogen-bonding on the relative stabilities of the various types of conformers of glycine and N-alkylated glycines. Comparisons of the relative energies of the various NMG and DMG conformers that have different types and number of hydrogen bonds (H-bonds) reveal the importance of hydrogen bonds to the stability of the different types of conformers. For NMG, conformer Ib which has two types of H-bonds and a dipole moment of 1.2 debyes is the most stable. Conformer Ib is similar to that of the most stable conformer of glycine. For DMG, on the other hand, IIc is the most stable conformer. IIc has a dipole moment of 5.6 debyes (compared to a value of 1.1 debyes for another of its conformers, Ic) and only one H-bond which involves the carboxylic acid and amino functionalities. The stability of IIc is attributed to the relative strength of the type H-bond formed — a similar type H-bond of glycine and NMG is predicted to be weaker. Thus, for a particular conformer, the relative strength and number of possible H-bonds that can be formed, and not necessarily the magnitude of the dipole moment, play key roles in the relative stability of amino acid conformers in the gas phase.     

Conformational studies of Phe-rich foldamers by VCD spectroscopy and ab initio calculations

Employing VCD spectroscopy, we demonstrate that the structural behavior of the oligomers Boc-(L-Phe-L-Oxd)(n)-OBn is similar from n = 2 to n = 6; ab initio calculations for the n = 1 case provide physical insight into the conformational properties. Further information is gained by IR, (1)H NMR, and ECD spectroscopies. ECD spectra suggest the presence of different conformations between n = 1 on one side and longer chain foldamers on the other side. VCD and absorption IR spectra in methanol solutions can be interpreted as indicative of a PPII structure. In the case of Boc-L-Phe-L-Oxd-OBn, VCD spectra in CCl(4) and detailed DFT computational analysis allow one to demonstrate that the most populated conformers exhibit backbone dihedral angles similar to those of a PPII geometry. This is a remarkable outcome, as we had previously demonstrated that the Boc-(L-Ala-D-Oxd)(n)-OBn series folds in a β-band ribbon spiral that is a subtype of the 3(10) helix.     

N-(acridin-9-yl)arenesulfonamides: Synthesis,quantum chemical studies and crystal structure analysis to establish the tautomeric preferences

The potentiality of the N-(acridin-9-yl)arenesulfonamide moiety as a hybrid pharmacophore due to the distinct pharmacological activities of acridines and aryl/heteroaryl sulfonamides prompts to synthesise N-(acridin-9-yl)arenesulfonamides and study their structural properties. Various N-(acridin-9-yl)arene/heteroarenesulfonamides were obtained through the development of a new methodology adopting the Pd₂(dba)₃-catalyzed CN bond formation strategy for the reaction of 9-chloloroacridine with arene/heteroarenesulfonamides. The 1H and ¹³C NMR spectra suggest these N-(acridin-9-yl)arene/heteroarenesulfonamides to exist solely as the sulfonimide tautomer rather than anticipated sulfonamide form and was confirmed by the single crystal XRD analysis of one of the newly synthesized compounds. The quantum chemical studies rationalized this tautomeric preference revealing that the sulfonimide tautomers are more stable than the sulfonamide tautomers by ?0.67 to ?5.12?kcal/mol in the gas phase. In the solid state, the sulfonimide tautomer is stabilized by intermolecular hydrogen bond between NH?OS and π? π stacking between the acridine rings.     

The coordination chemistry of the catalytic zinc ion in alcohol dehydrogenase studied by ab initio quantum chemical calculations

The coordination chemistry of the zinc ion in the active site of alcohol dehydrogenase has been studied by the ab initio Hartree–Fock method. Geometry optimizations were performed using analytical gradients and basis sets of double-zeta quality. Correlation effects were included at the MP 2 level. The active site was modeled by Zn(HS)₂XL(H₂O)_0–2, where X denotes ammonia or imidazole and L denotes water, methanol, ethanol, or the corresponding aldehydes or anions. It is shown that with uncharged L-ligands the four-coordinate complexes are about 20, 17, and 40kJ/mol more stable than are the corresponding three-, five-, and six-coordinate complexes, respectively. If the L-ligand is negatively charged, only the four-coordinate complexes are stable. These results suggest that the active-site zinc ion in alcohol dehydrogenase prefers a coordination number of four during the catalytic reaction, especially when the nonprotein ligand is negatively charged. Ligand exchange at the zinc ion is likely to proceed by an associative mechanism with intermittent formation of a five-coordinate complex. The results lend no support to mechanistic proposals attributing an important catalytic role to a negatively charged five-coordinate hydroxide or alkoxide ligand. © 1994 John Wiley & Sons, Inc.     

Computational studies of the cationic aluminium(chloro) hydroxides by quantum chemical ab initio methods

Cationic aluminium(chloro) hydroxide complexes with two to four aluminium atoms were studied using quantum chemical methods. Complexes were studied in both gas and liquid phase. The liquid environment was modeled by using a conductor-like screening model (COSMO). COSMO calculations were carried out as a single point calculation at the optimized gas phase structures. Water (epsilon = 78.54) was used as the solvent. The minimum energy structures obtained from the gas phase studies were mostly compact cyclic structures. Aluminium preferred to be five-coordinated in oxygen rich clusters. Core oxygen preferred three-fold coordination but in the largest clusters the four-coordinated oxygen was observed. Water reacted dissociatively with hydrogen poor clusters. The COSMO calculations showed that the optimal structures of cationic aluminium(chloro) hydroxides tend to be more open in the liquid than in the gas phase.     

Photoionization of C(4) molecular beam: ab initio calculations

Large computations are performed on the C(4) (+) cation in order to characterize its stable isomers and its lowest electronic excited states using configuration interaction methods and large basis sets. Several stable isomers are found including a linear C(4) (+)(l-C(4) (+)), a rhombic C(4) (+)(r-C(4) (+)) (or cyclic), and a branched (d-C(4) (+)) structure. Our calculations show a high density of electronic states for all of these isomers favoring their interactions. By combining the present ab initio data and those on neutral C(4), the l-C(4)(X)+hnu-->l-C(4) (+)(X(+))+e(-), d-C(4)(X)+hnu-->d-C(4) (+)(X(+))+e(-), and r-C(4)(X)+hnu-->r-C(4) (+)(X(+))+e(-) vertical photoionization transition energies are computed at 10.87, 10.92, and 10.77 eV, respectively. Photoionizing a C(4) molecular beam results on an onset at 10.4-10.5 eV and then to a linear increase of the signal due to the opening of several ionization channels involving most of the C(4) and C(4) (+) isomers and electronic states.     

Study on the behavior of energy convergence in ab initio crystal orbital calculations

Summary This article studies the dependence on the cutoff scheme of ab initio crystal orbital calculations with no long-range correction. We have thoroughly studied the Namur cutoff and cell-wise cutoff schemes through calculations of polyethylene and LiH chains. The Namur cutoff gives the fastest energy convergence with respect to the number of neighbors (N ₀). The energy convergence behavior with respect to N ₀ depends on the basis set. The Namur cutoff shows the fastest convergence with the STO-3G basis set, intermediate convergence with the MINI basis set, and the slowest convergence with the (7s4p/3s) basis set. The cell-wise cutoff shows exactly the reverse order of the Namur cutoff. The Namur cutoff destroys the translational symmetry. Both the Namur cutoff and cell-wise cutoff schemes introduce slight asymmetry on the two equivalent C-C bonds of polyethylene when calculating with a C₂H₄ unit cell. The asymmetry with the Namur cutoff can be made to disappear by increasing N ₀ a little. The calculations on two different unit-cell structures of trans-polyacetylene show the effect of the cutoff scheme on the total energy. Only the symmetric cutoff energies are the same. Disagreement related to the Namur cutoff disappears at N ₀ = 20, however, that related to the cell-wise and modified symmetric cutoff schemes remains at N ₀ 20. The optimized geometry and vibrational frequency are not as sensitive to the cutoff method except with the symmetric cutoff. A compilation of all results shows that the Namur cutoff is the superior cutoff scheme when calculating the insulator using the minimal basis set, especially the STO-3G basis set.     

Electronic structures of low-lying Bu excited states in trans-oligoenes: Pariser-Parr-Pople and ab initio calculations

Two lowest-lying excited singlets with B(u) symmetry of all-trans-oligoenes, the well-known ionic 1(1)B(u)(+) state as well as the "hidden" ionic-covalent-mixed 1(1)B(u)(-) state, are calculated within both the Pariser-Parr-Pople (PPP) model at full configuration interaction (FCI) level and ab initio methods. The vertical excitation energies as well as wavefunctions from PPP-FCI calculations are found to be in good agreement with those from high-level multi-reference methods, such as multi-reference complete active space self-consistent field (CASSCF) with second order perturbative corrections (CASPT2), multi-reference M?ller-Plesset perturbation theory (MRMP), and complete active space valence bond theory (CASVB). The oscillator strengths from PPP calculation are in good agreement with spectroscopy experiments. The relatively small oscillator strength of 1(1)B(u)(-) is due to the approximate electron-hole symmetry of this state. In addition, the bond lengths in both states are found to show remarkable relativity with the bond orders calculated with ground state geometries, which suggests a possible strategy for initial guess in geometry optimization of excited states.     

1,5-Diamino-1H-1,2,3,4-tetrazolium picrate: X-ray molecular and crystal structures and ab initio MO calculations

The crystal and molecular structures of 1,5-diamino-1H-1,2,3,4-tetrazolium picrate (DATP) were determined by X-ray diffraction analysis. The tetrazolium cation in DATP has a structure with protonated N4 atom of the ring. Two amino groups in the cation are found to be rather different. The 5-amino group lies in the plane of the tetrazole ring and valence angles around the N atom are close to 120°, which indicates sp² hybridization of atomic orbital of the nitrogen atom. In contrast, valence angles around the N atom of the 1-amino group are close to tetrahedral angle, which suggests sp³ hybridization. The exocyclic C-N bond in the cation is substantially shorter than that in 1,5-diaminotetrazole. The obtained results indicate a conjugation between the π-system of the tetrazole ring and the 5-amino group. The results of ab initio calculations of electronic structure and relative stability for various tautomeric forms of protonated 1,5-diaminotetrazole using MP2/6-31G* and B3LYP/6-31G* levels of theory are in a good agreement with X-ray data and show that there are differences in σ-electron overlap populations for the C-N bonds in the cation in DATP, while π-electrons are delocalized.