MP2 study on the hydrogen bonding interaction between 5-hydroxy-5-methylhydantoin and DNA bases: A,C, G,T

The 5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this study, we present the hydrogen bonding base pairs involving 5-OH-5-Me-dHyd bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: 5-OH-5-Me-dHyd:G>5-OH-5-Me-dHyd:A>5-OH-5-Me -dHyd:C~5-OH-5-Me-dHyd:T.     

MP2 study on the hydrogen-bonding interaction between 5-fluorocytosine and DNA bases: A,C, G,T

The 5-fluorocytosine (5-FC) is a fluorinated cytosine analog that is used as an antifungal agent. In this work, we present the hydrogen-bonding base pairs involving 5-FC bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis set superposition error, using the full Boys–Bernardi counterpoise correction scheme. Hydrogen-bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decreases in the following order: 5-FC:G > 5-FC:C > 5-FC:A > 5-FC:T.     

MP2 study on the hydrogen-bonding interaction between 5-hydroxymethyl-uracil and DNA bases: A,C, G,T

The 5-hydroxymethyl-uracil (HmU) is a product of oxidative attack on the methyl group of thymine in DNA. In this work, we present the hydrogen bonding complexes formation involving HmU bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys-Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: HmU:A > HmU:G > HmU:C > HmU:T.     

MP2 study on the hydrogen-bonding interaction between 5-fluorouracil and DNA bases: A,C,G,T

The 5-fluorouracil is a pyrimidine analog effective in the treatment of cancer. In this work, we present the hydrogen-bonding base pairs involving 5-FU bound to the four bases in DNA: adenine, cytosine, guanine, and thymine. Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error, using the full Boys-Bernardi counterpoise correction scheme. Hydrogen-bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: 5-FU:A > 5-FU:G > 5-FU:T > 5-FU:C.     

Hydrogen-bonding interaction of 5,6-dihydrouracil with RNA bases: DFT and MP2 studies

5,6-Dihydrouracil (DHU) is a rare pyrimidine base naturally occurring in tRNAs, it differs from the base uracil due to the saturation of the C₅–C₆ bond. This work presents the interaction energies of complexes formation involving DHU bound to the natural RNA bases adenine (A), uracil (U), guanine (G), and cytosine (C). Full geometry optimization has been performed for the studied complexes by B3LYP/6-31+G(d,p) and MP2/6-31+G(d,p) calculations. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. We find that the stability order is DHU:G > DHU:A > DHU:C  DHU:U.     

MP2 study on the hydrogen-bonding interaction between O 4-methylthymine and DNA bases: A,C, G,and T

The O ⁴-methylthymine (m⁴T) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this study, we present the hydrogen-bonding base pairs involving m⁴T bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error, using the full Boys–Bernardi counterpoise correction scheme. Hydrogen-bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: m⁴T:G > m⁴T:A > m⁴T:C > m⁴T:T.     

Revealing the physical nature and the strength of charge‐inverted hydrogen bonds by SAPT(DFT), MP2, SCS‐MP2, MP2C,and CCSD(T) methods

The physical nature of charge‐inverted hydrogen bonds in H₃XH YH₃ (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)‐based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS‐MP2, MP2C, and CCSD(T) methods utilizing dimer‐centered aug‐cc‐pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge‐inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: . It is confirmed that the aug‐cc‐pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole‐ζ quality. Considerably large binding energies suggest potential usefulness of charge‐inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ‐ and π‐hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge‐inverted hydrogen bond would become the first described case of a hydride‐triel bond. © 2017 Wiley Periodicals, Inc.     

Matrix-isolation FT-IR and DFT theoretical studies of the intramolecular hydrogen bonding in Mannich bases

FT-IR Ar-matrix isolated spectra were studied for dichloro- (Cl₂-MB) and tetrachloroderivatives (Cl₄-MB) of the ortho Mannich base. The spectra were analyzed based on the DFT calculated frequencies and intensities and compared with those recorded in CCl₄ solution in the region of the ν(OH) and ν(OD) vibrations. The matrix-isolated spectra are characterized by narrower ν(OH) and ν(OD) bands with much better resolved fine structure than in solution. The fine structure originates from the anharmonic coupling with the low frequency modes as well as from Fermi resonance. The ν(OD) band shapes can be reproduced exclusively by assuming the Fermi resonance with overtones and summation of the frequencies of modes into which the bridge atoms are involved. The frequency isotopic ratio (ISR) is for both compounds 1.33 while the half-width ratios are equal to 1.82 and 1.94, for Cl₂-MB and Cl₄-MB, respectively.     

MP2, DFT and ab initio calculations on thioxanthone

Density functional theory (DFT), HF and MP2 calculations have been carried out to investigate thioxanthone molecule using the standard 6-31+G(d,p) basis set. The results of MP2 calculations show a butterfly structure for thioxanthone. The calculated results show that the predicted geometry can well reproduce the structural parameters. The predicted vibrational frequencies were assigned and compared with experimental IR spectra. A good harmony between theory and experiment is found. The theoretical electronic absorption spectra have been calculated using CIS method. ¹³C and ¹H NMR of the title compound have been calculated by means of B3LYP density functional method with 6-31+G(d,p) basis set. The comparison of the experimental and the theoretical results indicate that density functional B3LYP method is able to provide satisfactory results for predicting NMR properties.     

On the accuracy of DFT-SAPT, MP2, SCS-MP2, MP2C, and DFT+Disp methods for the interaction energies of endohedral complexes of the C(60) fullerene with a rare gas atom

Selected points on the potential energy surface for the complexes Rg@C(60) (Rg = He, Ne, Ar, Kr) are calculated with various theoretical methods, like symmetry-adapted perturbation theory with monomers described by density functional theory (DFT-SAPT), supermolecular M?ller-Plesset theory truncated on the second order (MP2), spin-component-scaled MP2 (SCS-MP2), supermolecular density functional theory with empirical dispersion correction (DFT+Disp), and the recently developed MP2C method that improves the MP2 method for long-range electron correlation effects. A stabilization of the endohedral complex is predicted by all methods, but the depth of the potential energy well is overestimated by the DFT+Disp and MP2 approaches. On the other hand, the MP2C model agrees well with DFT-SAPT, which serves as the reference. The performance of SCS-MP2 is mixed: it produces too low interaction energies for the two heavier guests, while its accuracy for He@C(60) and Ne@C(60) is similar to that of MP2C. Fitting formulas for the main interaction energy components, i.e. the dispersion and first-order repulsion energies are proposed, which are applicable for both endo- and exohedral cases. For all examined methods density fitting is used to evaluate two-electron repulsion integrals, which is indispensable to allow studies of noncovalent complexes of this size. It has been found that density-fitting auxiliary basis sets cannot be used in a black-box fashion for the calculation of the first-order SAPT electrostatic energy, and that the quality of these basis sets should be always carefully examined in order to avoid an unphysical long-range behavior.     

Anion-arene adducts: C-H hydrogen bonding, anion-pi interaction, and carbon bonding motifs

This article summarizes experimental and theoretical evidence for the existence of four distinct binding modes for complexes of anions with charge-neutral arenes. These include C-H hydrogen bonding and three motifs involving the arene-pi system-the noncovalent anion-pi interaction, weakly covalent sigma interaction, and strongly covalent sigma interaction.     

A new non-symmetric N(OH)3 species: Comparison with the C3 species and thermochemistry at the HF,DFT, MP2, MP4 and CCSD(T) levels of theory

A new non-symmetric N(OH)₃ species more stable than the C₃ structure is found at Density Functional Theory (B3PW91, B3LYP), MP2, MP4 and CCSD(T) levels with extended basis sets. C₁ and C₃ structures are qualitatively different from those of the As(OH)₃ molecule. Energy differences and interconversion barriers become smaller with increasing inclusion of electronic correlation. However at the MP2, MP4 and CCSD(T) levels, these differences increase with basis set quality. ZPE corrections lead to barrier collapse but only at the CCSD(T)/AVTZ level. The C₁ and C₃ MP2/AVTZ infrared spectra are given for future studies.     

MP2 study on the hydrogen-bonding interactions between 4-thiouracil and four RNA bases

The 4-thiouracil (s⁴U) is a sulphur-containing analog of uracil, a natural component of RNA. In this work, we present the interaction energies of complexes formation involving s⁴U bound to the four bases in RNA: adenine (A), uracil (U), guanine (G), and cytosine (C). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. We find that the order of stability for the base pairs is s⁴U: G > s⁴U: A > s⁴U: U ~ s⁴U: C.     

NMR,MP2, and DFT study of thiophenoxyketenimines (o‐thio‐Schiff bases): Determination of the preferred form

Five new thiophenoxyketinimines have been synthesized. ¹H and ¹³C NMR spectra as well as deuterium isotope effects on ¹³C chemical shifts are determined, and spectra are assigned. DFT and MP2 calculations of both structures, chemical shifts, and isotope effects on chemical shifts are done. The combined analysis reveals that the compounds are primarily on a zwitterionic form with an NH⁺ and a S⁻ group and with a little of the neutral form mixed in. Very strong intramolecular hydrogen bonding is found and very high NH chemical shifts are observed. The theoretical calculations show that calculations at the MP2 level are best to obtain correct “C═S” chemical shifts.     

LCAO–MO studies on hydrogen bonding: The interaction between carbonyl and hydroxyl groups

Potential curves that show the energy dependence of hydrogen bonds between carbonyl and hydroxyl groups on the O? H bond length, on the distance between the molecules, and on the angle between the functional groups have been calculated with the CNDO /2 method. The results are presented for a small model system–formaldehyde/water—and for the dimer of formic acid. Good agreement is obtained with the available experimental data. The influence of the molecular geometry on the calculated results is discussed.     

Vibrational spectra and harmonic force fields of pyrrolidine derivatives: comparison between HF, MP2 and DFT force fields

Infrared and Raman spectra are reported for the isotopic species of pyrrolidine-d₀ (PY) and -d₁ and for N-methylpyrrolidine-d₀ (NMP), -d₂, -d₃ and -d₈. A complete assignment of the experimentally observed bands to normal modes is presented and discussed in particular in the CH/CD stretching region. The molecular structures and harmonic force fields were calculated ab initio at the Hartree–Fock (HF), the second order Møller–Plesset (MP2) and the density functional theory (DFT) level with the 6-31G* basis set. The force fields were fitted by use of 7 (PY) and 4 (NMP) independent scale factors. The spectra calculated with the DFT force fields are in better agreement with the experiment than those calculated by the MP2 and HF force fields. Though some scaled fundamental frequencies show larger deviations from the experimental ones, the mean percentage deviations of calculated frequencies from experimental fundamentals are less than 2.6% for all isotopic species of PY and NMP under study. The results indicate that density functional theory is a reliable tool to get a deeper insight in the assignment of vibrational spectra and the nature of normal modes of pyrrolidine derivatives.     

The effect of oxidation on the stability of G:C base pair: a MP2 study

The base-pairing energies of eleven oxidized G:C base pairs were characterized by Møller–Plesset perturbation theory. The analysis was focused on the base pairs consisting of guanine and one of the following cytosine derivatives: G:C1 (5-hydroxycytosine); G:C2 (5-hydroxyuracil); G:C3 (5,6-dihydroxy-cytosine); G:C4 (5,6-dihydroxy-uracil); G:C5 (cytosine glycol);G:C6 (isodialuric acid); G:C7 (uracil glycol), and the base pairs between cytosine and one of the following guanine derivatives: G8:C (8-oxo-guanine); G9:C (6-enol-8-keto-guanine); G10:C (xantho-sine); and G11:C (8-hydroxy-guanine). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys-Bernardi counterpoise correction scheme. The results obtained show that the interaction energies of the base pairs decrease in the following order: G8:C > G:C5 ~ G:C1 > G:C3 ~ G:C ~ G11:C > G:C2 > G:C4 > G:C7 > G:C6 > G10:C > G9:C.     

Interaction between Non-Conjugated Chromophores: 5,6-Dimethylidene-exo-2-norborneol, 5,6-Dimethylidene-exo,exo-2,3-norbornanediol and 5,6-Dimethylidene-2-norbornanone

Preparation of the title compounds 11 , 12 and 13 is described. Preliminary kinetic results indicate that the hydroxyl substituents in 11 and 12 have a very small retardation effect on the Diels-Alder reactivity of 2,3-dimethylidene-norbornane. The keto group in 13 exerts a larger retardation effect, although it is much smaller than the retardation effect introduced by an exo-5,6-epoxide ring in 2,3-dimethylidene-norbornane.