DFT STUDY OF LONG BONDS IN RADICAL CATIONS OF SUGAR [610255]

DFT STUDY OF LONG BONDS IN RADICAL CATIONS OF SUGAR
DERIVATIVES

Mihai -Cosmin Pascariu1,2,3*, Madian Rafail ă4, Mihai Medeleanu4,
Ramona Curpan5, Liliana P ăcureanu5, Nicolae Dincă6, Eugen Șișu1*

1“Victor Babeș” University of Medicine and Pharmacy of Timișo ara, Faculty of Medicine, 2
Eftimie Murgu Sq., RO -300041, Timișoara, Romania
2National Institute of Research and Development for Electrochemistry and Condensed Matter
– INCEMC Timișoara , 144 Dr. Aurel Păunescu Podeanu, RO -300569, Timișoara, Romania
3“Vasil e Goldiș” Western University of Arad, Faculty of Pharmacy, 86 Liviu Rebreanu, RO –
310045, Arad, Romania
4University Politehnica Timișoara, Faculty of Industrial Chemistry and Environmental
Engineering, 6 Vasile Pârvan Blvd., RO -300223, Timișoara, Romania
5Institute of Chemistry Timișoara of Romanian Academy, 24 Mihai Viteazul Blvd., RO –
300223 , Timișoara, Romania
6“Aurel Vlaicu” University of Arad, Faculty of Food Engineering, Tourism and
Environmental Protection, 2 Elena Drăgoi, RO -310330, Arad, Romania
e-mail: [anonimizat], [anonimizat]

Abstract
We have performed DFT computations on radical cations of several monosaccharide
derivatives , using the STO -3G and 3 -21G basis sets . The obtained long bond lengths were
compared with the value s we have previously obtained using the RM1 and PM7 semi –
empirical methods. The applied DFT method s offered smaller values for the long bond
lengths , attaining only 1.6÷1.7 Å. Also, in contrast with t he simple STO -3G basis , which
shows some exceptions, the more advanced 3 -21G basis set always places the long bond in
the correct C4 -C5 position , as suggested by the EI -MS analyses.

Introduction
Long bonds appear to be a ubiquitous feature in the molecular radical cations produced during
the positive mode elec tron ionization mass spectrometry ( EI-MS) analysis of compounds
possessing vicinal electron donor substituents, like diols or diethers [1]. Carbohydrates are an
example of such compounds . While s emi-empirical methods [2,3] give long bond lengths for
radica l cations that are likely to be exaggerated , DFT computations are known to be more
moderate in this respect. To verify this assumption we have performed DFT analyses on
radical cations of five monosaccharide derivatives , which contain the furanose moiety (Fig.
1): 1,2:5,6 -di-O-isopropylidene -α-D-glucofuranose (DAG), 1,2:5,6 -di-O-isopropylidene -α-D-
allofuranose (DAA lo), 1,2:5,6 -di-O-isopropylidene -α-D-galactofuranose (DAGal), 2,3:5,6 -di-
O-isopropylidene -α-D-mannofuranose (α -DAM) and 2,3:5,6 -di-O-isopropylidene -β-D-
mannofuranose (β-DAM). All these species show, during the EI -MS analysis, a preference for
the breaking of the C4 -C5 bond, with the formation of the 2,2-dimethyl -1,3-dioxolan -4-ylium
oxocarbenium ion , which exhibits a high intensity m/z = 101 peak [2,3].

Experimental
All structures were initially modeled using the HyperChem 8.0.10 software [4]. The starting
neutral molecules, obtained after “MM+” pre -optimization, were optimized with the RM1
semi -empirical method [5]. The radical cations were obtained from these structu res and were
pre-optimized with RM1. As for “Spin Pairing”, RHF operators were used for neutral
molecules, while UHF operators were employed for radical -cations. The SCF “Convergence

limit” was set at 10-5, without using the “Accelerate convergence” proced ure. For geometry
optimization, the “Polak -Ribière (conjugate gradient)” algorithm was selected with a RMS
gradient of 0.01 kcal (Å mol)-1, the molecules being considered in vacuum (conditions similar
to those found in EI -MS detectors).
Theoretical calcula tions were finally performed using the Gaussian 09 software [6]. The
equilibrium geometries of the radical cations were optimized using the density functional
theory (DFT) method at the B3LYP/STO -3G or B3LYP/3 -21G level s. The B3LYP hybrid
functional was us ed for these studies because of convention and the successful use to model a
range of gas -phase reactions .

Figure 1. Structure of the studied compounds

Results and discussion
The DFT results regarding the enthalpy of f ormation ( ΔfH0) at 0 and 298 K, the Gibbs free
energy (Δ fG0) at 298 K and some bond lengths are given in Tables 1 and 2, while the O4 -C4-
C5, O5 -C5-C4 and O4 -C4-C5-O5 angle values are given in Table 3 .

Table 1. Results obtained for the radical cations using the B3LY P/STO -3G level of theory

Compound ΔfH0 0 K
(kcal mol-1) ΔfH0 298 K
(kcal mol-1) ΔfG0 298 K
(kcal mol-1) Bond length (Å)
C1-C2 C2-C3 C3-C4 C4-C5 C5-C6
DAG * -1967.33 -1984.8 -2311.0 1.583 1.594 1.613 1.637 1.575
DAAlo -1977.86 -1996.1 -2324.1 1.576 1.589 1.606 1.628 1.574
DAGal -1961.96 -1979.3 -2305.4 1.586 1.635 1.585 1.617 1.580
α-DAM -1969.30 -1987.0 -2314.2 1.586 1.575 1.592 1.619 1.573
β-DAM -1972.65 -1990.7 -2319.0 1.595 1.581 1.585 1.609 1.566
*optimization was started from 3 -21G geometry

Table 2. Resul ts obtained for the radical cations using the B3LYP/3 -21G level of theory

Compound ΔfH0 0 K
(kcal mol-1) ΔfH0 298 K
(kcal mol-1) ΔfG0 298 K
(kcal mol-1) Bond length (Å)
C1-C2 C2-C3 C3-C4 C4-C5 C5-C6
DAG -1250.31 -1267.4 -1592.9 1.536 1.529 1.538 1.650 1.531
DAAlo -1254.74 -1272.5 -1599.7 1.542 1.553 1.572 1.648 1.541
DAGal -1250.40 -1267.8 -1594.7 1.536 1.527 1.548 1.712 1.534
α-DAM -1250.86 -1268.4 -1595.7 1.527 1.547 1.562 1.562 1.537
β-DAM -1252.40 -1269.9 -1597.0 1.553 1.556 1.556 1.597 1.537

The molecular models for the considered radical cations (B3LYP/3 -21G) are shown in Fig. 2 .

DAG DAAlo

DAGal

α-DAM β-DAM

Figure 2. Molecular models obtained after running the B3LYP/3 -21G optimization

The observed position of the long bond generally coincides with our previous results obtaine d
using the RM1 and PM7 semi -empirical methods.

Table 3 . Angle values (degrees) obtained for the radical cations

Compound STO -3G 3-21G
O4-C4-C5 O5-C5-C4 O4-C4-C5-O5 O4-C4-C5 O5-C5-C4 O4-C4-C5-O5
DAG 113.4 108.1 117.6 105.8 105.3 176.2
DAAlo 115.8 108.2 -134.7 111.1 108.3 -162.1
DAGal 112.6 111.6 71.2 112.1 108.5 -42.7
α-DAM 112.5 110.7 -138.5 107.3 110.2 -161.5
β-DAM 110.7 110.2 -143.5 109.5 107.5 166.8

Conclusion
In contrast with our previous results [2,3] obtained using the RM1 and PM7 semi -empirical
methods, which give long bonds of slightly over 2 Å, the DFT method s applied offered long
bonds of maximum 1.712 Å. The 3 -21G basis set seems to give better results with respect to
the long bond location, when compared with the more simple STO -3G basis set.

Acknow ledgements
This work was supported by the Romanian National Authority for Scientific Research
(CNCS -UEFISCDI) through project PN -II-PCCA -2011 -142. Part of the research was
performed at the Center of Genomic Medicine of the “Victor Babeș” University of Medi cine
and Pharmacy of Timisoara, POSCCE 185/48749, contract 677/09.04.2015.

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