Search results for "Ab initio"
showing 10 items of 990 documents
Determination of the lowest-energy oxidation site in nucleotides: 2'-deoxythymidine 5'-monophosphate anion.
2006
High level ab initio computations anticipate nucleobases as the most favorable sites for oxidation in nucleotides. At the CASPT2 level, the lowest ionization channel for the 2'-deoxythymidine 5'-monophosphate anion is related to a pi-orbital of the thymine base. The present findings lead to revision of the recent assignments of the photodetachment photoelectron spectra of mononucleotide anions in the gas phase and support the classical view of the nucleobase being the main actor in the oxidation process of both nucleosides and nucleotides.
Cooperative Effects in Aminothiols: Acid-Base Equilibria and the Molecular Structure of 2-(N, N-Dimethylaminomethyl)thiophenol
2008
Abstract 2-(N,N-Dimethylaminomethyl)thiophenol, (1, HL), is present as a non-zwitterionic aminothiol in the solid state, exhibiting an intramolecular S-H···N hydrogen bond. The S···N distances of the two independent molecules in the asymmetric unit are 2.929(10) and 3.050(10) Å. This structural feature is also present in an ab initio (MP2/6-31G*) optimized molecular structure. The investigation of the hydrogen bond by ab initio methods supports an n(N)-σ *(S-H) interaction as the reason for this bond type. On the basis of data from potentiometric acid-base titrations of a 0.01 M aqueous solution of [H2L]Cl with a 0.1 M aqueous solution of sodium hydroxide, values of 4.09±0.01 and 11.50±0.01…
DNA nucleobase properties and photoreactivity: Modeling environmental effects
2009
Abstract The accurate ab initio quantum chemical (QM) method multiconfigurational second-order perturbation (CASSPT2)/complete active space self-consistent field (CASSCF) has been used in conjunction with molecular mechanics (MM) procedures to compute molecular properties and photoinduced reactivity of DNA/RNA nucleobases (NABs) in isolation and within a realistic environment, in which the double helix strand, the aqueous media, and the external counterions are included. It is illustrated that the use of an MM model is helpful both to account for short- and long-range effects of the system surrounding the QM molecular core and to provide the proper structural constraints that allow more acc…
THEORETICAL INSIGHTS ON O2 AND CO ADSORPTION ON NEUTRAL AND POSITIVELY CHARGED GOLD CLUSTERS
2006
With the aim of understanding the elementary steps governing the oxidation of CO catalyzed by dispersed or supported gold nanoclusters, the adsorption of molecular species, such as O2 and CO, on model neutral and positively charged clusters (Au(n)(m+) n = 1, 9, and 13; m = 0, 1, and 3) has been studied using an ab initio approach. The computed structural and thermodynamic data related to the binding process show that molecular oxygen interacts better with neutral clusters, acting as an electron acceptor, while CO more strongly binds to positively charged species, thus acting as an electron donor.
Predominance of 2-arylhydrazones of 1,3-diphenylpropane-1,2,3-trione over its proton-transfer products
2001
2-Phenylhydrazones of 1,3-diphenyl-1,2,3-trione are the dominant tautomeric form detected in chloroform solution by 15N NMR chemical shifts. The substituent in the phenylhydrazone moiety does not affect this tautomeric preference. The substituent effect is transmitted effectively only to the hydrazone nitrogen and hydrogen atoms. Ab initio calculations show that the ketohydrazone tautomer is really very much favoured over its proton-transfer products in chloroform solution. The same tautomer was also detected in the crystal state by X-ray crystallography. Copyright © 2001 John Wiley & Sons, Ltd.
Regio- and stereoselective synthesis of constrained enantiomeric β-amino acid derivatives
2008
Abstract Chlorosulfonyl isocyanate addition to (−)- and (+)-apopinene furnished monoterpene-fused β-lactams in highly regio- and stereospecific reactions. β-Lactams 5 and 13 exhibited reactivities similar to those of the cycloalkane-fused analogs and were easily converted to the β-amino acid and its protected derivatives. The base-catalyzed isomerization of the cis -amino ester afforded the corresponding trans -amino acid enantiomers in excellent yields. The complete isomerization is explained by the stability difference, which was estimated by ab initio calculations between the cis- and trans -diastereomers.
Theoretical study of the OH addition to the β-pinene
2004
The initial step of the mechanism of the OH + β-pinene gas-phase reaction was investigated by means of ab initio calculations. Four different possibilities for the OH addition to the double bond are discussed, corresponding to the addition on each C atom of the double bond, and for each one, either the syn or anti OH attack to the two methyl groups on the (bi)cyclic molecule. Energy barriers calculated at the QCISD(T)/6-31G(d) level of theory on UMP2/6-31G(d) optimised structures, show that there are preferred orientations for the OH addition under atmospheric conditions of temperature and pressure.
Bonding in the heavy analogue of hydrogen cyanide: the curious case of bridged HPSi.
2010
The bonding of firstand second-row elements differ dramatically. The simplest unsaturated silicon hydrides Si2H2 and Si2H4 exhibit quite unusual geometries [1] compared to the analogous hydrocarbon molecules. For example, the most stable form of Si2H2 is nonplanar with C2v symmetry and two bridging H atoms, in sharp contrast to linear acetylene, HC! CH. Phosphorus and nitrogen share many of the same bonding characteristics, but P prefers single over multiple bonds. For these reasons, it may be difficult to predict the most stable isomeric arrangement, even for a small molecule with a single Por Si atom and especially when it contains both. Silicon–phosphorus bonds are important in materials…
1,2-Dipolar addition model for the cytoprotective activity of selected α,β-unsaturated compounds with CO functionality: an ab initio study
2001
Abstract The mechanism of the addition of a nucleophile (an alkylthiol group) to a double bond of α,β-unsaturated systems in the gas phase was explored. In this study, intermediates of the reaction were also investigated using ab initio calculations (RHF/6-31G ∗ and MP2/6-31+G ∗ ). Our results indicate that direct dipolar attack of the S–H group of an alkylthiol on the CC double bond is a reasonable reaction path. The present results represent, therefore, additional support for our hypothesis. This suggests that the mechanism of cytoprotection might be mediated, at least in part, by a reaction between the olefinic acceptor and the sulfhydryl-containing groups of the mucosa.
DLPNO-CCSD(T) scaled methods for the accurate treatment of large supramolecular complexes
2017
In this work, we present scaled variants of the DLPNO-CCSD(T) method, dubbed as (LS)DLPNO-CCSD(T) and (NS)DLPNO-CCSD(T), to obtain accurate interaction energies in supramolecular complexes governed by noncovalent interactions. The novel scaled schemes are based on the linear combination of the DLPNO-CCSD(T) correlation energies calculated with the standard (LoosePNO and NormalPNO) and modified (Loose2PNO and Normal2PNO) DLPNO-CCSD(T) accuracy levels. The scaled DLPNO-CCSD(T) variants provide nearly TightPNO accuracy, which is essential for the quantification of weak noncovalent interactions, with a noticeable saving in computational cost. Importantly, the accuracy of the proposed schemes is…