Conformational, Spectroscopic, and Molecular Dynamics DFT Study of

Article pubs.acs.org/JPCA

Conformational, Spectroscopic, and Molecular Dynamics DFT Study of Precursors for New Potential Antibacterial Fluoroquinolone Drugs Sandra Dorotíková,† Kristína Plevová,‡ Lukás ̌ Bučinský,*,† Michal Malček,† Peter Herich,† Lenka Kucková,† Miroslava Bobeničová,† Stanislava Šoralová,§ Jozef Kožíšek,† Marek Fronc,† Viktor Milata,‡ and Dana Dvoranovᆠ†

Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37 Bratislava, Slovak Republic ‡ Institute of Organic Chemistry, Catalysis and Petrochemistry, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37 Bratislava, Slovak Republic § Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovak Republic S Supporting Information *

ABSTRACT: Biological activity, functionality, and synthesis of (fluoro)quinolones is closely related to their precursors (for instance 3-fluoroanilinoethylene derivatives) (i.e., their functional groups, conformational behavior, and/or electronic structure). Herein, the theoretical study of 3-fluoroanilinoethylene derivatives is presented. Impact of substituents (acetyl, methyl ester, and ethyl ester) on the conformational analysis and the spectral behavior is investigated. The B3LYP/6-311++G** computational protocol is utilized. It is found that the intramolecular hydrogen bond N−H···O is responsible for the energetic preference of anti (a) conformer (anti position of 3-fluoroanilino group with respect to the CC double bond). The Boltzmann ratios of the conformers are related to the differences of the particular dipole moments and/ or their dependence on the solvent polarity. The studied acetyl, ethyl ester, and methyl ester substituted fluoroquinolone precursors prefer in the solvent either EZa, ZZa, or both conformers equally, respectively. In order to understand the degree of freedom of rotation of the trans ethyl ester group, B3LYP/6-311G** molecular dynamic simulations were carried out. Vibrational frequencies, electron transitions, as well as NMR spectra are analyzed with respect to conformational analysis, including the effect of the substituent. X-ray structures of the precursors are presented and compared with the results of the conformational analysis.

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INTRODUCTION 3-Fluoroanilinoethylene derivatives belong to precursors of quinolones. Quinolones possess a variety of biological activities, including antimicrobial,1 antiviral (anti-HIV),2,3 and antimalarial effects.4 Nowadays, the fluoroquinolones play a specific role in medicine, being widely used for the treatment of infections caused by both Gram-positive5,6 or Gram-negative6−8 pathogens. Moreover, fluoroquinolones have been demonstrated to possess antitumor activity,9,10 hand-in-hand with interesting mechanical effect on the DNA molecule.11−14 DNA gyrase and DNA topoisomerase IV are both sensitive to the 4-quinolone class of antibacterial compounds in vitro. This activity of quinolones is the result of the inhibition of the supercoiling of DNA catalyzed by the enzyme DNA gyrase. Emami et al.15 and Shen16 have proposed drug−DNA models which imply hydrogen-bond type interactions between the DNA unpaired bases and the quinolone, as well as a stacked dimerization of the drug. Stereochemistry is becoming very important in such interactions (i.e., the orientation of the substituents can be critical for the activity of the agents). © XXXX American Chemical Society

Manipulations of the basic molecule, including replacement of hydrogen with fluorine, substitution on the cyclic amine residue, and the addition of new residues on the quinolone ring, have led to improved breadth and potency of antibacterial activity and pharmacokinetics. Thus, the primary attention was foremostly focused on the investigations of structure−activity relationships of fluoroquinolones. Nowadays, the attention turns to innovative novel reaction pathways which lead to the synthesis of novel derivatives, emphasizing the role of the precursors from which the substances are mainly prepared using the modified Gould-Jacobs reaction.17,18 Newly synthesized 3-fluoroquinolones have been prepared from precursors bounded with different substituents R1 and R2, such as −COOC2H5, −COOCH3, and −COCH3.19 The structure of these precursors of fluoroquinolones is summarized in Table 1. Received: June 26, 2014 Revised: September 4, 2014

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Table 1. Overview of the Fluoroquinolone Precursors under Study

Figure 1. Molecular structures of studied anti conformers of P1.

In accordance with the literature data,20,21 previous quantumchemical studies were oriented exclusively toward the spectroscopic and tautomeric characterization of quinolones. A closer theoretical study of (fluoro)quinolone precursors using standard DFT computational protocols and a subsequent comparison to the experiment19 has not been carried out yet. The fluoroquinolone precursors are well-known as push−pull ethylenes.22−24 Similar push−pull ethylenes prefer the anti (a) orientation of 3-fluoroanilinegroup with respect to the CC double bond of ethylene comparing to the syn (s) orientation.25−27 Intramolecular hydrogen bond between the amino hydrogen and carbonyl oxygen from the acetyl or methyl/ethyl ester group is found to be a key factor for the energetically preferred conformers.28 Hence, the E or Z isomers (acetyl/methyl ester/ethyl ester CO group in the trans or cis position toward the amino group) are the most significant for the conformational analysis of such compounds. Molecular structures of the studied anti conformers are shown in Figure 1. Challenge in these push−pull substituted fluoroquinolone precursors is the admixture of concurrent interactions. The πconjugation prefers a planar structure of the push−pull systems. The planar structure is furthermore stabilized by the hydrogen bond between the amino hydrogen and the carbonyl oxygen from the acetyl29 or methyl/ethyl ester30 group. On the other hand, sp3 hybridization of the amino nitrogen and the hydrogen−hydrogen repulsion prefer different nonplanar geometries. Hence, these systems are well-suited for a real test of standard computational protocols. In addition, the

biological activity of synthesized (fluoro)quinolones is determined by their precursors, as mentioned above (i.e., their functional groups conformational behavior and/or electronic structure). In general, β-keto carboxylic acid moiety (positions C10 and C11) is essentially required for hydrogenbonding interactions with DNA. Furthermore, the antibacterial and/or DNA-binding activity as well as pharmacokinetic properties of quinolones depend on the nature of peripheral substituents and their spatial arrangements.15 The position of the fluorine atom and the orientation of the group which does not undergo the cyclization to quinolone are also directly related to the conformational behavior of the initial precursor and might be directly related to the biological activity of the target quinolone. Herein, DFT conformational analysis of diethyl 2-[(3fluorophenylamino)methylene]malonate (P1), dimethyl 2[(3-fluorophenylamino)methylene]malonate (P2), and 3-[(3fluorophenylamino)methylene]pentane-2,4-dione (P3) push− pull compounds19 is reported, focusing presumably on fluorine in position 3 (C3−F) (see Table 1). The outcome of the conformational analysis is critically confronted with the obtained X-ray structures. In addition, to obtain a better insight on the conformational behavior of the molecules (especially for the trans ethyl ester group of P1 compound), the method of molecular dynamics (MD) is utilized. Consequently, the theoretical investigation of conformational analysis, vibrational spectra, electronic transitions, and NMR chemical shifts are presented. The obtained results are analyzed with respect to B

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Table 2. Crystal Data of the Precursors under Study precursor empirical formula formula weight (g mol−1) temperature (K) wavelength (Å) crystal system, space group unit cell dimension

volume (Å3) Z, calc density (mg m−3) absorption coefficient (mm−1) F(000) crystal size (mm3) θ range for data collection (deg) reflections collected/unique completeness to 2θ = 25.00 refinement method data/restraints/parameters GoF on F2 final R indices [I > 2σ(I)] R indices (all data) Δρmax and Δρmin (e Å−3)

P1

P2

P3

C14H16FNO4 281.28 100(1) 0.71073 triclinic, P1̅ a = 8.7649(5) Å b = 8.7954(7) Å c = 9.007(1) Å α = 90.566(9)° β = 95.610(8)° γ = 100.043(6)° 680.15(12) 2, 1.373 0.109 296 0.689 × 0.222 × 0.072 4.115 to 26.371 7910/2637 95.9%

C12H12FNO4 253.23 293(2) 0.71073 triclinic, P1̅ a = 7.1117(3) Å b = 7.1194(4) Å c = 12.0150(7) Å α = 74.345(5)° β = 85.823(4)° γ = 79.083(4)° 575.01(5) 2, 1.463 0.121 264 0.998 × 0.533 × 0.166 4.525 to 24.713 14108/1952 96.1% full-matrix least-squares on F2

C12H12FNO2 221.23 293(2) 0.71073 triclinic, P1̅ a = 6.1162(3) Å b = 9.6371(5) Å c = 10.2412(5) Å α = 108.298(4)° β = 98.083(4)° γ = 100.432(4)° 550.90(5) 2, 1.334 0.102 232 0.961 × 0.790 × 0.092 4.098 to 24.702 7308/1865 95.8%

1952/0/165 1.032 R1 = 0.0354 wR2 = 0.0953 R1 = 0.0388 wR2 = 0.0986 0.237 and −0.200

1865/133/147 1.044 R1 = 0.0413 wR2 = 0.1099 R1 = 0.0505 wR2 = 0.1172 0.149 and −0.181

2637/0/191 1.041 R1 = 0.0534 wR2 = 0.1284 R1 = 0.0683 wR2 = 0.1398 0.357 and −0.302

the experimentally measured spectra and the obtained crystal structures.

75 MHz for 1H, 19F, and 13C nuclei. All details of FT-IR, UV− vis, and NMR measurements are described in Plevová et al.19

EXPERIMENTAL METHODS Crystallization of P1 precursor was performed via a slow diffusion between a double layer of water (antisolvent) into dimethyl sulfoxide (P1 containing solution). P2 precursor was crystallized out of chloroform by a slow diffusion of vapors of antisolvent (hexane). Crystals of P3 were prepared by a slow evaporation of solvent from the mixture of chloroform/ methanol in ratio 10:1 (vol). All crystals of the studied precursors were colorless, and the precipitation took 1 week. Xray diffraction data were collected on Oxford Diffraction Gemini R diffractometer equipped with Ruby CCD detector and Mo Kα sealed-tube source at 100 or 293 K. Data collection and reduction was performed with Oxford Diffraction CrysAlis PRO version 1.171.37.31.31 Crystal structures were solved by direct methods with SHELXS-2008 and refined by least-squares procedure on F2 with SHELXL-2013.32 DIAMOND was used for the molecular graphics.33 IR spectra in the region of 4000−700 cm−1 were recorded on the Nicolet model NEXUS 470 FT-IR spectrometer. The FTIR spectra in CHCl3 were measured in Omni-cell assembling with KBr liquid Omni windows with lead spaces. The UV−vis spectra of the investigated compounds in CHCl3 and dimethyl sulfoxide (DMSO) were recorded using a UV−vis−NIR UV 3600 spectrophotometer (Shimadzu, Japan) with a 1 cm square quartz cell. All NMR spectra were measured on the Agilent 600 MHz VNMRS spectrometer operating at frequencies 600 and 150 MHz for 1H, 19F, and 13C nuclei and on an Agilent 300 MHz VNMRS spectrometer operating at frequencies 300 and

COMPUTATIONAL DETAILS The geometry optimization was performed at the B3LYP34−37/ 6-311++G**38 level of theory using Gaussian03.39 Solvent effects in DMSO and CHCl3 solutions were approximated by the integral equation formalism polarizable continuum model (IEFPCM),40,41 and a full conformational analysis of the fluoroquinolone precursors under study was performed. A vibrational analysis was used to confirm that the optimal geometry corresponds to the energy minimum (no imaginary vibrations) and to obtain the vibrational spectra. TD-DFT electronic transitions42,43 were computed for each relevant conformer using the same solvent as in the experimental measurements (DMSO and CHCl3). The 50 lowest electron excitations from the ground state were accounted for. 13C, 1H, and 19F NMR chemical shifts were calculated using the individual gauges for atoms in molecules (IGAIM)44,45 and the gauge-including atomic orbital (GIAO)46−49 approaches as embedded in Gaussian 03. TMS (1H and 13C NMR) and CFCl3 (19F NMR) were employed as NMR standards in the determination of theoretical chemical shifts. Atomic charges from the quantum theory of atoms in molecules50−52 have been obtained from the AIMAll package.53 The molecular dynamics (MD) in vacuo calculations of P1 precursor were performed at the B3LYP/6-311G** level of theory using NWChem.54 A Berendsen thermostat55 was employed, and the temperature was set to 300 K with a time step of 0.001 ps. The optimized ZZa P1 conformer was used as the starting geometry in the MD simulation because of the higher Boltzmann ratio

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Figure 2. ORTEP drawing of (a) P1 (disordered F2 and H5A atoms were omitted) (b) P2 and (c) P3 showing the labeling of the nonhydrogen atoms with 50% probability thermal displacement ellipsoids.

interactions are also observed (see Table S-1 of the Supporting Information). These interactions form one-dimensional (1D) (P1), two-dimensional (2D) (P3), or three-dimensional (3D) (P2) chains in the particular crystal structures as shown in Figure S-1 of the Supporting Information. Conformational Analysis. The outcome of the B3LYP/6311++G**/IEFPCM conformational analysis of the studied P1−P3 compounds is compiled in Table 4. Only the anti conformers of the studied precursors are considered (syn conformers are not energetically favored and hence omitted from any further discussion). The Boltzmann ratios of the EEa and ZEa conformers are less than 3%; thus, these conformers and their properties are for brevity left out from any further discussions. Following the obtained results, the impact of the substituents on the conformational ratios of the precursors under study is substantial (Table 4). Apparently, the acetyl group is preferring the EZa conformer (P3 precursor), while the ethyl ester substituted P1 precursor prefers the ZZa conformer, regardless of the solvent model inclusion. Thus, the different ratios for the P1 and P3 precursors can be assigned to the different contribution of the mesomeric or induction effects (push− pull π-conjugation) and the steric repulsion effects of the particular substituents. In this respect, the intramolecular hydrogen bond between the oxygen of CO (ester or acetyl group) and the hydrogen of the N−H group as well as the degree of electron density delocalization are also to be mentioned. Conversely, the Boltzmann ratio of the methyl ester substituted P2 is significantly affected by the inclusion of the solvent effects in comparison with P1. This discrepancy can

(approximately 85% in vacuo, see Table 4). The full time duration of the MD simulation at 300 K was 16.5 ps.

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RESULTS AND DISCUSION X-ray Structure. ORTEP format drawings of the P1−P3 precursors (data shown in Table 2) are shown in Figure 2. All compounds (P1−P3) crystallize in the triclinic P1̅ space group with one molecule in the asymmetric unit. The P1 compound is in the ZZa conformation in the crystal, where the fluorine atoms are disordered in the ratio of 88:12 with respect to the 5 to 3 position in the benzene ring, respectively. Structures of P2 and P3 are in the EZa conformation, and the fluorine atom is in the position 5. The comparison of the experimental and theoretical geometries will be discussed within the section on theoretical results. Intra- and intermolecular hydrogen bonds play an important stabilizing role in the studied structures (P1−P3) in the solid state. Dominant feature of each structure is the strong intramolecular hydrogen bond between the N7 and O2 atoms of the amino and carbonyl groups creating a sixmembered ring (Table 3). Additional intermolecular C−H···O

Table 3. Intramolecular Hydrogen-Bond Geometry Parameters for Precursors (Å, deg) Obtained from X-ray precursor

D−H···A

d(D−H)

d(H···A)

d(D···A)