Wyniki wyszukiwania - BazTech

1

Charakterystyka mocy poszczególnych wiązań wodorowych w parach zasad DNA

Szatyłowicz Halina, Sadlej-Sosnowska Nina, Jezierska Aneta

Wiadomości Chemiczne

|

2019

|

[Z] 73, 1-2

53--74

EN

The main idea of the current review is to present methods useful to characterize the strength of individual hydrogen bonds in nucleic acids base-pairs. In the paper, the Authors discuss the energy definition of intermolecular interactions taking into account the presence of one intermolecular hydrogen bond (HB) as well as the situation when several intermolecular interactions (namely intermolecular hydrogen bonds) are present. In the Section 2 of the review a general overview of methods developed to estimate the strength of the individual intermolecular hydrogen bond in DNA/RNA base-pairs is presented. Thus, the reader can find detailed information on the methods used so far: the rotational method (2003), compliance constants method (2004), the EML equation application (2006), the atom replacement method (2007), the estimation of hydrogen bond energy on the basis of electron density (calculated by using the AIM theory) at BCP values (2009), the application of NBO method (2010), the comparison of HB strength based on the last two approaches (2015) and the application of coordinates interaction approach (2017). It should be emphasized, that these methods allow to estimate the strength of intermolecular interactions both in the model base-pairs and in other systems with several intermolecular hydrogen bonds. The discussion of the presented methods is supported by Tables 1-10, containing numerical values characteristics of the strength of the particular HB, and Figures 1–2. The section 3 contains a critical comparison of results based on the presented methods. Concluding remarks are given in the last Section.

2

Theoretical investigations on the structural, spectroscopic, electronic and thermodynamic properties of (3-Oxo-3H-benzo[f]chromen-1yl) methyl N,N-dimethylcarbamodithioate-1ex

Kara M., Evecen M., Özdogan T.

Materials Science Poland

|

2017

|

Vol. 35, No. 3

560--575

EN

Hartree-Fock and Density Functional Theory (B3LYP, B3PW91) calculations for the ground state of (3-Oxo-3Hbenzo[ f]chromen-1-yl) methyl N,N-dimethylcarbamodithioate have been presented and the calculated structural parameters and energetic properties have been compared with the available X-ray diffraction data. The vibrational frequencies have been calculated using optimized geometry of the molecule. The conformational properties of the molecule have been determined by computing molecular energy properties, in which torsional angle varied from -180° to +180° in steps of 10°. Moreover, natural bond orbital analysis and atomic charge analysis have been performed. Besides, HOMO and LUMO energies have been calculated and their pictures have been presented. Finally, molecular electrostatic potential and thermodynamic properties have been calculated. It is seen that the obtained theoretical results agree well with the available experimental values. In all the calculations, except for optimization and vibrational calculations, B3LYP level of theory with 6-311++G(d,p) basis set has been used.

3

A theoretical study on 2-chloro-5-(2-hydroxyethyl)-4-methoxy-6-methylpyrimidine by DFT/ab initio calculations

Gumus H. P., Tamer O., Avci D., Atalay Y.

Materials Science Poland

|

2015

|

Vol. 33, No. 2

369--380

EN

Quantum chemical calculations have been performed to study the molecular geometry, H-1 and C-13 NMR chemical shifts, conformational, natural bond orbital (NBO) and nonlinear optical (NLO) properties of the 2-chloro-5-(2-hydroxyethyl)-4methoxy-6-methylpyrimidine molecule in the ground state using DFT and HF methods with 6-311++G(d,p) basis set. The optimized geometric parameters and H-1 and C-13 NMR chemical shifts have been compared with the experimental values of the title molecule. The results of the calculations show excellent agreement between the experimental and calculated frequencies at B3LYP/6-311++G(d,p) level. In order to provide a full understanding of the properties of the title molecule in the context of molecular orbital picture, the highest occupied molecular energy level (E-HOMO), the lowest unoccupied molecular energy level (E-LUMO), the energy difference (Delta E) between EHOMO and ELUMO, electronegativity (chi), hardness (eta) and softness (S) have been calculated using B3LYP/6-311++G(d, p) and HF/6-311++G(d,p) levels. The calculated HOMO and LUMO energies show that the charge transfer occurs within the title molecule.

4

Strukturalne konsekwencje wiązania wodorowego

Krygowski T.M., Szatyłowicz H.

Wiadomości Chemiczne

|

2011

|

[Z] 65, 11-12

953-974

EN

Hydrogen bonding belongs to the most important chemical interactions in life and geochemical processes as well as in technologies, that is documented in many review articles [1-10], monographs [11-17] and numerous publications. Figure 1 presents how "popular" are studies concerning hydrogen bonds (the term H-bond/bonding/bonded in a title, key-words or in abstract) in the last decade. First information about H-bond formation appeared at the end of XIX and a few other at beginning of XX centuries [19-24]. Most common definition of H-bonding stems from Pauling [27], whereas the newest IUPAC definition was published very recently [26]. Most frequently H-bonding is experimentally described by geometry parameters [28, 32] - results of X-ray and neutron diffraction measurements, but NMR and IR/Raman spectroscopies are also in frequent use. Characteristic of interactions by H-bonding is usually discussed in terms of energies [29-31], with use of various quantum chemical theories [54-57] and applications of various models as AIM [35, 41, 42, 45-48] and NBO [43, 44] which allowed to formulate detailed criteria for H-bond characteristics [35, 48]. H-bonds are classified as strong, mostly covalent in nature [7, 29, 34], partly covalent of medium strength [35] and weak ones, usually non-covalent [7, 29, 34, 35]. Theoretical studies of H-bonding mainly concern equilibrium systems, however simulation of H-bonded complexes with controlled and gradually changing strength of interactions [61-71] are also performed. The latter is main source of data referring to effect of H-bonding on structural properties: changes in the region of interactions, short and long-distance consequences of H-bonding. Application of the model [61] based on approaching hydrofluoric acid to the basic center of a molecule and fluoride to the acidic one, (Schemes 2 and 3) allows to study changes in molecular structure of para-substituted derivatives of phenol and phenolate [62, 64] in function of dB…H, or other geometric parameter of H-bond strength (Fig. 2). It is also shown that CO bond lengths in these complexes is monotonically related to H-bond formation energy and deformation energy due to H-bond formation [65]. Alike studies carried out for para-substituted derivatives of aniline and its protonated and deprotonated forms [77, 78, 81] give similar picture (Fig. 3). AIM studies of anilines [77, 78] lead to an excellent dependence of logarithm of electron density in the bond critical point and geometric parameter of H-bond strength, dB…H presented in Figure 4. Substituents and H-bond formation affect dramatically geometry of amine group [66] in H-bonded complexes of aniline as shown by changes of pyramidalization of bonds in amine group (Fig. 5). Some short- and long-distance structural consequences of H-bonding are shown by means of changes in ipso angle (for amine group) in the ring and ipso-ortho CC bond lengths (Fig. 6). Moreover, the mutual interrelations are in line with the Bent-Walsh rule [84, 86]. Changes of the strength of H-bonds in complexes of p-substituted aniline and its protonated and deprotonated derivative are dramatically reflected by aromaticity of the ring66 estimated by use of HOMA index [87, 88] (Fig. 7), where strength of H-bonding is approximated by CN bond lengths. Scheme 4 presents application of the SESE [91] (Substituent Effect Stabilization Energy) for description in an energetic scale joint substituent and H-bond formation effects.

5

Intermolecular Interactions in o-Tolidinium Dichloride Dihydrate: X-ray Structural and Quantum Mechanical Study

Kruszynski R.

Polish Journal of Chemistry

|

2009

|

Vol. 83, nr 4

615-623

EN

The title compound, C14H22Cl2N2O2, (I), was determined by X-ray crystallography, and the intermolecular interactions energy was calculated in terms of Natural Bond Orbital analysis. The (I) is composed from 3,3'-dimethyl-(1,1'-biphenyl)-4,4'-diammonium cation two chloride anions and two water molecules. The mid point of the linking aromatic rings C—C bond is located on two fold rotation axis, and thus asymmetric unit is occupied by half of cation, one anion and one water molecule. All the interatomic distances and angles in (I) are normal. The almost planar aromatic rings are inclined at 38.82(4) graduate. In the structure exists intermolecular N—HźźźO, N—HźźźCl, O—HźźźCl hydrogen bonds with bonding energy ranging from 4 to 26 kcal/mol. All hydrogen bonds of (I) in terms of first level graphs create D motifs. No face-to-face stacking interactions are observed.