Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions

Hydrogen-bonding interactions often make substantial contributions to the specificity of protein-nucleic acid complexes. Using a geometric modeling approach, we previously identified 28 possible doubly hydrogen-bonded interactions to the four unpaired RNA bases. Here we present interaction energies of these models, calculated by ab initio quantum chemical methods, and describe a correlation between the computed energies and observed frequencies of the interactions. In general, interactions with charged side chains show the most favorable energies. An Asp/Glu-G interaction may be especially favorable for recognition of unpaired guanines in RNAs. Asn and Ser/Thr/Tyr side chains are calculated to make iso-energetic interactions to the Hoogsteen face of adenine, but Asn-A interactions are much more common with DNA than RNA, and Ser/Thr/Tyr-A interactions are more common with RNA than DNA. Examination of the known interactions suggests that Ser/Thr/Tyr may be accommodated in a wider variety of protein contexts at RNA-protein interfaces. With these calculated intrinsic affinities, it should be possible to better assess the contributions of bidentate hydrogen-bonding interactions to RNA- and DNA-binding specificity.     

Benzooxirene. Ab initio calculations

Ab initio calculations have been performed on benzooxirene, the corresponding oxo carbene (“ketocarbene”), and the transition state linking the two. At the highest level used, QCISD(T)/6-31G^*//MP2(FULL)/6-1G^* with MP2(FULL)/ 6-31G^* zero point energy corrections, the relative energies of the oxirene, the transition state and the carbene are 0, 24.6, and −17.8 kJ mol⁻¹. Correlation energy effects are very important in this system: at the QCISD(T) level the oxirene lies above the carbene, as at the MP4 and HF levels, but at the MP2 level the ordering is reversed. Benzooxirene is probably slightly nonplanar: the HF/6-31G^* geometry is C_2v but the MP2(Fermi contact)/6-31G^* geometry is C_s with a 6-/3-ring coplanarity deviation of about 6.9 °, although in the MP2(FULL)/6-31G^* geometry this is reduced to about 3.1 °.     

Ab initio calculations on urea

Multiconfiguration wave functions constructed from contracted Gaussian-lobe functions have been found for the ground and valence-excited states of urea. ICSCF molecular orbitals of the excited states were used as the parent configurations for the CI calculations except for the ¹A₁(π → π*) state. The ¹A₁(π → π*) state used as its parent configuration an orthogonal linear combination of natural orbitals obtained from the second root of a three-configuration SCF calculation. The lowest excited states are predicted to be the n π → π* and π → π* triplet states. The lowest singlet state is predicted to be the n π → π* state with an energy in good agreement with the one known UV band at 7.2 eV. The π → π* singlet state is predicted to be about 1.9 eV higher, contrary to several previous assignments which assumed the lowest band was a π → π* amide resonance band. The predicted ionization energy of 9.0 eV makes this and higher states autoionizing.     

Ab initio calculations on porphin

Ab initio SCF calculations are reported for the porphin molecule. The positions of the central protons have been optimized, and the equilibrium geometry is found to be a linear NH ? HN arrangement. The NH vibrational frequencies have been computed and are compared to experimentally measured quantities. Several low ionized states have also been studied in separate spin-restricted SCF calculations. The lowest state is found to have B_1u symmetry with an ionization potential of 8.0 eV.     

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell et al. force field is confirmed and this indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.     

Ab initio molecular orbital calculations

A series of non-empirical calculations on furan, pyrrole and 1,2,5-oxadiazole are reported in which the effect of polarisation functions added to the minimal 7s 3p basis on each atom is studied. The effect on these planar molecules is largely through the rather than the-system. A comparison with the results of work with scaled functions is reported. Both series are shown to lead to much improved agreement with the electron spectroscopy energy levels. The effect on the dipole moments of these changes in basis is more variable but, with the exception of furan, the agreement with experiment is improved in the present method.

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Zusammenfassung Für die Moleküle Furan, Pyrrol und 1,2,5-Oxadiazol wurde eine Reihe von nichtempirischen Rechnungen durchgeführt, in denen der Einfluß von zusätzlichen Polarisationsfunktionen zur minimalen 7s 3p-Basis an jedem Atom untersucht wird. Die Ergebnisse werden mehr durch die Art der Beschreibung des Systems der-Elektronen als durch diejenige der-Elektronen beeinflußt. Ein Vergleich mit den Ergebnissen bei Verwendung skalierter Funktionen wird durchgeführt. Beide Reihen von Ergebnissen zeigen eine verbesserte Übereinstimmung zu den Energiemeßwerten der Elektronenspektroskopie. Die Änderungen des berechneten Dipolmoments bei derartigen Basisvariationen sind größer als bei früheren Methoden. Die Übereinstimmung mit dem Experiment wird, mit Ausnahme von Furan, jedoch verbessert.

     

Ab initio quantum-mechanical calculations on trifluoromethylamine

Extensive ab initio molecular-orbital calculations were carried out on trifluoromethylamine (TFM) to elucidate changes in geometry and electronic structure upon fluorination. The calculations show that the decomposition of CF₃NH₂ is slightly endoenergetic, and the heats of atomization of CF₃NH₂ and CH₃NH₂ show decreased stability of the species upon fluorination. Characteristic of CF₃NH₂ is a highly polar, strong, short CN bond. More limited calculations were carried out on CF₃OH and CH₃OH, and the electronic structure of CF₃OH is found to be generally similar to that of CF₃NH₂. The reduced basicity of the fluorinated amine cannot be ascribed to the inductive effect; the enhanced acidity of the fluorinated alcohol reflects the weakening of the OH bond. No evidence leads to a confirmation of the existence of nitrogen–fluorine hyperconjugation in the fluorinated amine.     

Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.     

硫代甲酰胺双聚体的量子化学计算

在MP2/6 31G(d)和MP2(FC)/6 311 G(d,p)水平上,对硫代甲酰胺(HC-SNH2)及其3种构型双聚体进行几何全优化计算,经振动频率分析,确认为势能超曲面上的稳定驻点.然后在MP2/6 311 G(2df,2p)水平上进行单点能计算和基组重叠误差(BSSE)校正以获得相互作用能.并利用自然键轨道(NBO)理论和分子中的原子(AIM)理论探讨HCSNH2之间相互作用的本质.     

Ab initio calculations of NMR chemical shifts

The nuclear magnetic resonance chemical shift is one of the most powerful properties available for structure determination at the molecular level. A review of advances made in the ab initio calculation of chemical shielding during the past five years is presented. Specifically, progress in the areas including the effects of an unpaired electron, electron correlation, and relativistic effects into ab initio chemical shielding calculations, the tensor nature of the chemical shift, and intramolecular and intermolecular effects on the chemical shift will be covered.     

Ab initio calculations of silicon-halogen-silicon double bridges

Summary Structure and stability of molecular clusters modelling halogen (F, Cl) double bridges between silicon atoms, H₃SiF₂SiH₃ (1), H₃SiF₂SiF₃ (2), H₃SiCl₂SiH₃ (3), and H₃SiCl₂ SiCl₃ (4), have been investigated by an ab initio pseudopotential method. Asymmetrical bridges Si-X...Si with one strong Si-X bond and one weak Si...X bonding interaction (X=F, Cl) result from the geometry optimization using the LP-31 G basis set. Dissociation energy calculations using the MP2/LP-31G*//LP-31G procedure and considering the basis set superposition error provide a decrease of stability of the structures in the order2>4>3>1. The results are discussed with respect to formation and decomposition of halogenated reaction overlayers formed during the etching of silicon by halogen atoms.

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Ab-Initio-Berechnungen von Silizium-Halogen-Silizium-Doppelbrücken

Zusammenfassung Struktur und Stabilität von molekularen Clustern, die Halogen(F, Cl)-Doppelbrücken zwischen Siliziumatomen modellieren, H₃SiF₂SiH₃ (1), H₃SiF₂SiF₃ (2), H₃SiCl₂SiH₃ (3) und H₃SiCl₂SiCl₃ (4), werden mittels eines Ab-Initio-Pseudopotentialverfahrens untersucht. Bei der Geometrieoptimierung unter Verwendung des LP-31 G-Basissatzes ergeben sich asymmetrische Brücken Si-X...Si mit einer starken Si-X-Bindung und einer schwachen bindenden Si...X-Wechselwirkung (X=F, Cl). Dissoziationsenergieberechnungen durch das MP2/LP-31 G*//LP-31 G-Verfahren unter Berücksichtigung des Basissatzüberlagerungsfehlers liefert eine abnehmende Stabilität der Cluster in der Reihenfolge2>4>3>1. Die Resultate werden im Zusammenhang mit der Bildung und dem Zerfall von halogenierten Reaktionsschichen, welche während des reaktiven Ätzens von Silizium mit Halogenatomen gebildet werden, diskutiert.

     

Ab initio calculations on blocked Pro-Ala dipeptides

The effect of the chirality of the amino acid at position i + 2 on a β-turn was investigated by a grid scan ab initio calculation on the Ac- -Pro- -Ala-NH₂ and Ac- -Pro- -Ala-NH₂ blocked dipeptides. Th6-31G basis set was used to estimate the effect of the alanyl side chain on the conformation of the peptide backbone in a blocked dipeptide as a simple, but complete model for a reverse turn. This study provides a quantum mechanical evaluation of the ability of the NH at the i + 3 residue to form the H-bond that closes the 10 membered ring which stabilizes the turn. The lowest energy of all 64 probed conformations of the -Ala containing peptide corresponded to a good type II β-turn with a hydrogen bond distance between the acetyl oxygen and the amide terminal hydrogen of 2.21 Å. A comparison with the nonblocked dipeptide ab initio study indicates that the presence of the end blocks enhances the propensity of the -Ala-containing dipeptide for a type II β-turn, but does not seem to enhance the propensity of the -Ala-containing dipeptide for a type I β-turn. The energies and geometric parameters for the lowest four optimized conformations identified by the grid scan search for each molecule have been calculated.     

Ab initio calculations on the structure of monomeric and dimeric formic acid

Experiments show changes in the carbon-oxygen bond lengths when a carboxylic acid dimerizes. To see how these changes are depicted in the electronic structure, a series of ab initio calculations have been made on monomeric and dimeric formic acid. Both systems have been examined through energy optimalization and through a Mulliken population analysis.The experimental changes can be qualitatively explained by the calculations, however, the quantitative agreement is not as good as desired.The calculations on monomeric formic acid give valuable information on the possibility of separately computing the different structural parameters.     

Ab initio CI calculations on free-base porphin

Ab initio configuration interaction (CI ) calculations were carried out on low-lying singlet and triplet π–π* states and ionized states of free-base porphin. We take into account single and double excitations from σ and π electrons in the CI calculations. The composite natural orbitals were employed in order to reduce the size of orbital set to be used in the CI . The calculated excitation energies were in good agreement with experimental values. The use of split-valence-type basis and the inclusion of correlation effects of σ electrons were proved to be important to describe the low-lying π–π* states, especially the Soret band.     

Ab initio calculations on bismuth cluster polycations

Ab initio calculations on bismuth polycationic species of the types Bi(n(n-2))+, Bi(n(n-4))+, and Bi(n(n-6))+ (n = 3 - 12) were performed at the Hartree-Fock and density functional theory levels in order to investigate their general properties and the applicability of Wade's rules on bismuth polycations. Some exceptions to Wade's rules were encountered, and, moreover, several predicted and calculated minima show only meta-stable behavior. The bonding in bismuth polycations is characterized by a high degree of electron delocalization and "three-dimensional aromaticity".     

Ab initio calculations on CICN and ONCI

Ab initio calculations are presented for the molecules CICN and ONCI with optimization of all geometric parameters. Calculated equilibrium geometries for CICN are in good agreement with microwave data; however, the calculated N-Cl distance in ONCI is about 0.1 Å shorter than obtained by electron diffraction. Orbital energies are calculated by means of Koopmans' theorem and also by ΔSCF calculations. The importance of relaxation energy is shown by comparing the calculated orbital energies with experimental data from photoelectron spectra of the valence levels.     

Ab initio calculations for the photoelectron spectra of vanadium clusters

We report ab initio calculations for the electronic and structural properties of V(n), V(n) (-), and V(n) (+) clusters up to n=8. We performed the calculations using a real-space pseudopotential method based on the local spin density approximation for exchange and correlation. This method assumes no explicit basis. Wave functions are evaluated on a uniform grid; only one parameter, the grid spacing, is used to control convergence of the electronic properties. Charged states are easily handled in real space, in contrast to methods based on supercells where Coulombic divergences require special handling. For each size and charge state, we find the lowest energy structure. Our results for the photoelectron spectra, using the optimized structure, agree well with those obtained by experiment. We also obtain satisfactory agreement with the measured ionization potential and electron affinity, and compare our results to calculations using an explicit basis.     

Ab initio cluster calculations of silica surface sites

Silica surface sites, which can be formed in cleavage processes, and their hydrolyzed counterparts are investigated with ab initio cluster calculations. Natural Bond Orbital (NBO) theory is used to characterize bonding around silica surface sites. Higher energy lone pairs of electrons on oxygen atoms either hyperconjugate to vicinal silanol/siloxane antibonding orbitals or backdonate electron density via donor–acceptor π-type bonding with participation of pd or p hybrids on silicon atoms. Upon substitution of hydroxyl groups of orthosilicic acid with silica monomers the strength of siloxane and silanol Si–O bonding increases as energies of bonding orbitals and contributions from p-orbitals decrease. Silanone sites and a complementary pair of silyl/siloxy radical sites are found to be the most stable geminal and single non-hydrolyzed sites, respectively. Atomic charges based on natural wavefunctions and on fitting to electrostatic potential, and characteristic bands of IR spectra associated with siloxane and silanol stretching vibrations of silica surface sites are reported.