Ar Matrix Research Articles

Tunneling Assists the 1,2‐Hydrogen Shift in N‐Heterocyclic Carbenes

AbstractAt room temperature, 1,2‐hydrogen‐transfer reactions of N‐heterocyclic carbenes, like the imidazol‐2‐ylidene to give imidazole is shown to occurr almost entirely (>90 %) by quantum mechanical tunneling (QMT). At 60 K in an Ar matrix, for the 2, 3‐dihydrothiazol‐2‐ylidene→thiazole transformation, QMT is shown to increase the rate about 105 times. Calculations including small‐curvature tunneling show that the barrier for intermolecular 1,2‐hydrogen‐transfer reaction is small, and QMT leads to a reduced rate of the forward reaction because of nonclassical reflections even at room temperature. A small barrier also leads to smaller kinetic isotope effects because of efficient QMT by both H and D. QMT does not always lead to faster reactions or larger KIE values, particularly when the barrier is small.

Trifluoromethylphenylcarbenes. Carbene-Carbene Interconversion on the Singlet Energy Surface and Rearrangement to Trifluorobenzocyclobutene, Trifluorostyrene, and Trifluoromethylfulvenallenes

The four isomeric α-, ortho-, meta-, and para-trifluoromethylphenylcarbenes were generated by photolysis of the corresponding 3-phenyl-3-trifluoromethyldiazirene 1 or the four isomeric trifluoromethylphenyldiazomethanes 2 and 4–6. The four corresponding triplet trifluoromethylphenylcarbenes 3 and 7–9 were observed by electron spin resonance (ESR) spectroscopy in Ar matrices at 14 K. The α- and ortho-carbenes 3 and 7 and the ortho- and para-carbenes 7 and 9 interconvert partially when generated by short-wavelength photolysis (350 nm) before intersystem crossing to the triplet states. The triplet states do not undergo further Carbene-Carbene interconversion. The interconversions are assumed to take place via the meta-trifluoromethylphenylcarbene 8. When the ortho- and para-carbenes are generated by long-wavelength photolysis (>450 nm), the discrete, non-interconverting triplet carbenes are observed in the ESR spectra. Flash vacuum thermolysis of the diazirene 1 at 500°C afforded a mixture of bis(trifluoromethyl)heptafulvalenes 11, bis(trifluoromethyl)stilbenes 12, and bis(trifluoromethyl)anthracenes 13, and the presence of their likely precursor(s), trifluoromethylcycloheptatetraene(s), was confirmed by a peak at 1830 cm–1 in the Ar matrix IR spectrum. In addition, at 700°C, four monomeric carbene rearrangement products were isolated and characterised, viz. 1,1,2-trifluorobenzocyclobutene 14, 1′,2′,2′-trifluorostyrene 15, and 1- and 2-trifluoromethylfulvenallenes 16 and 17.

Matrix isolation and DFT study of the conformations of diethylcarbonate

Conformations of diethylcarbonate (DEC) were studied using matrix isolation infrared spectroscopy. DEC was trapped in an Ar matrix at 12K, using both an effusive source maintained at 298 and 423K and a supersonic jet source. The experimental studies were supported by computations performed at the B3LYP/6-31++G** level of theory. The ground state conformer for DEC was found to have a “cc(tt)” geometry, where the ‘c’ refers to a cis orientation of the carbons attached to oxygen, while the ‘t’ in parenthesis refers to the trans orientation of the terminal carbon. In addition to the ground state conformer, our computations also indicated local minima corresponding to conformers with cc(tg±), cc(g±g∓) and cc(g±g±) geometries, listed in increasing order of energy. Natural bond orbital analysis was also performed to understand the role of delocalization interactions and steric effect on conformational stability.

Combined ab Initio Molecular Dynamics and Experimental Studies of Carbon Atom Addition to Benzene

Car-Parrinello molecular dynamics was used to explore the reactions between triplet and singlet carbon atoms with benzene. The computations reveal that, in the singlet C atom reaction, products are very exothermic where nearly every collision yields a product that is determined by the initial encounter geometry. The singlet C atom reaction does not follow the minimum energy path because the bimolecular reaction is controlled by dynamics (i.e., initial orientation of encounter). On the other hand, in a 10 K solid Ar matrix, ground state C((3)P) atoms do tend to follow RRKM kinetics. Thus, ab initio molecular dynamics (AIMD) results indicate that a significant fraction of C-H insertion occurs to form phenylcarbene whereas, in marked contrast to previous theoretical and experimental conclusions, the Ar matrix isolation studies indicate a large fraction of direct cycloheptatetraene formation, without the intermediacy of phenylcarbene. The AIMD calculations are more consistent with vaporized carbon atom experiments where labeling studies indicate the initial formation of phenylcarbene. This underlines that the availability of thermodynamic sinks can completely alter the observed reaction dynamics.

Tunable Diode Lasers as a Tool for Conformational Control: The Case of Matrix-Isolated Oxamic Acid

A tunable diode laser was applied as a source of narrowband near-infrared light used to manipulate the structure of the molecule of oxamic acid. Monomers of the most stable conformer I of the molecule, with the trans orientation of the O═COH group and the trans orientation of the O═CC═O fragment, were trapped from the gas phase in low-temperature argon, neon, and nitrogen matrixes. Monomers of oxamic acid, isolated in argon or neon matrixes, were then irradiated with narrowband near-IR light from the diode laser tuned at 6833 (Ar) or 6840 cm(-1) (Ne). Upon such irradiation another conformer, II, of oxamic acid was generated, with cis orientation of the O═COH group and trans orientation of the O═CC═O fragment. Both forms were identified by comparison of their experimental mid-IR spectra with the spectra theoretically calculated for I and II. Subsequent irradiation of the matrix at 6940 (Ar) or 6991 cm(-1) (Ne), where absorption appeared in the near-IR spectrum of the photoproduct, led to photoconversion of conformer II into form I. In a series of subsequent irradiations at 6833(Ar)/6840(Ne) cm(-1) and at 6940(Ar)/6991(Ne) cm(-1), the population of oxamic acid molecules was selectively shifted several times from I to II and vice versa. As far as we know, this is the first reported study where a tunable diode laser source of narrowband near-IR light was used to manipulate the structure of a molecule. Spontaneous II → I transformation was observed for Ne and Ar matrixes kept in the dark and at cryogenic temperature.

Acetamide as the model of the peptide bond: Nonadiabatic photodynamical simulations in the gas phase and in the argon matrix

The short-time photodynamics of acetamide in the gas phase and in the Ar-matrix starting from the first excited singlet S1 (n–π*) and S2 (π–π*) states was explored by the direct trajectory surface hopping method based on multiconfigurational ab initio calculations. For the n–π* state effect of embedding into Ar matrix employing hybrid QM/MM approach on the lifetime and dissociation paths was also discussed. The calculations show that nonadiabatic deactivation from the S1 to the ground state occurs within 785fs via the crossing seam related to the CN bond stretching MXS. The major products in the gas phase are NH2+CH3CO radicals which partially undergo further dissociation of the CH3CO or recombination to the parent molecule. The embedding of the molecule in the Ar matrix considerably suppresses the CN dissociation and prevents dissociation of the CH3CO radical.

3-Pyridazinylnitrenes and 2-Pyrimidinylnitrenes

Mild flash vacuum thermolysis of tetrazolo[1,5-b]pyridazines 8T generates small amounts of 3-azidopyridazines 8A (8aA, IR 2145, 2118 cm(-1); 8bA, 2142 cm(-1)). Photolysis of the tetrazoles/azides 8T/8A in Ar matrix generates 3-pyridazinylnitrenes 9, detected by ESR spectroscopy (9a: D/hc = 1.006; E/hc = 0.003 cm(-1)). Cyanovinylcarbenes 11, derived from 4-diazobut-2-enenitriles 10, are also detected by ESR spectroscopy (11a: D/hc = 0.362; E/hc = 0.021 cm(-1)). Carbenes 11 rearrange to cyanoallenes 12 and 3-cyanocyclopropenes 13. Triazacycloheptatetraenes 20 were not observed in the photolyses of 8. Photolysis of tetrazolo[1,5-a]pyrimidines/2-azidopyridmidines 18T/18A in Ar matrices at 254 nm yields 2-pyrimidinylnitrenes 19, observable by ESR, UV, and IR spectroscopy (19a: ESR: D/hc = 1.217; E/hc = 0.0052 cm(-1)). Excellent agreement with the calculated IR spectrum identifies the 1,2,4-triazacyclohepta-1,2,4,6-tetraenes 20 (20a, 1969 cm(-1); 20b, 1979 cm(-1)). Compounds 20 undergo photochemical ring-opening to 1-isocyano-3-diazopropenes 23. Further irradiation also causes Type II ring-opening of pyrimidinylnitrenes 19 to 2-(cyanimino)vinylnitrenes 21 (21a: D/hc = 0.875; E/hc = 0.00 cm(-1)), isomerization to cyaniminoketenimine 25 (2044 cm(-1)), and cyclization to 1-cyanopyrazoles 22. The reaction mechanisms are discussed and supported by DFT calculations on key intermediates and pathways. There is no evidence for the interconversion of 3-pyridazinylnitrenes 9 and 2-pyrimidinylnitrenes 19.

Vibrational Shifts of HXeCl in Matrix Environments

The hybrid quantum-classical simulations are performed to investigate the unusual vibrational spectral shifts of a noble-gas hydride HXeCl in matrix environments (in Ne, Ar, Kr, and Xe matrixes). The high-level ab initio calculations at the CCSD(T) level are employed to construct interaction potential energy surfaces between HXeCl and noble-gas atoms (Ne, Ar, Kr, and Xe). The configurations of noble-gas atoms are sampled by the Monte Carlo simulations and the vibrational levels of HXeCl in the presence of the surrounding noble-gas atoms are solved by the DVR approach. It is found that the H-Xe stretching frequencies are blue-shifted from the isolated gas-phase value in all matrix environments and that the relative blue shifts are in good agreement with the experimental results (Ne < Xe < Kr), demonstrating that the explicit treatment of matrix environments around HXeCl is essential to reproduce the observed unusual vibrational shifts.

Vibronic spectra of the p-benzoquinone radical anion and cation: a matrix isolation and computational study

The electronic and vibrational absorption spectra of the radical anion and cation of p-benzoquinone (PBQ) in an Ar matrix between 500 and 40,000 cm(-1) are presented and discussed in detail. Of particular interest is the radical cation, which shows very unusual spectroscopic features that can be understood in terms of vibronic coupling between the ground and a very low-lying excited state. The infrared spectrum of PBQ˙(+) exhibits a very conspicuous and complicated pattern of features above 1900 cm(-1) that is due to this electronic transition, and offers an unusually vivid demonstration of the effects of vibronic coupling in what would usually be a relatively simple region of the electromagnetic spectrum associated only with vibrational transitions. As expected, the intensities of most of the IR transitions leading to levels that couple the ground to the very low-lying first excited state of PBQ˙(+) increase by large factors upon ionization, due to "intensity borrowing" from the D0 → D1 electronic transition. A notable exception is the antisymmetric C=O stretching vibration, which contributes significantly to the vibronic coupling, but has nevertheless quite small intensity in the cation spectrum. This surprising feature is rationalized on the basis of a simple perturbation analysis.

C8H6 Thermal Chemistry. 7-Methylenecyclohepta-1,3,5-dienyne (Heptafulvyne) by Flash Vacuum Thermolysis–Matrix Isolation. Chemical Activation in the Rearrangements of Phenylenedicarbenes and of Benzocyclobutadiene to Phenylacetylene

Methylenecycloheptadienyne 11 (heptafulvyne) is obtained very cleanly by flash vacuum thermolysis (FVT) of the diazobenzocyclobutene precursor 8 at 400°C followed by isolation as a neat solid at 77 K or in an Ar matrix at 7–10 K. Compound 11 is a yellow solid, stable till ~–100°C in the neat state. The diazo compound itself (2) is observable by IR spectroscopy following mild decomposition of the tosylhydrazone salt 1 at 115°C. FVT of 8 at 200°C also generates diazo compound 2 as observed by IR spectroscopy and on-line mass spectrometry. FVT of 8 at 600–800°C causes rearrangement of 11 to phenylacetylene 12 and benzocyclobutadiene 13. Mechanisms for the rearrangements are proposed. Facile rearrangement of benzocyclobutadiene to phenylacetylene is ascribed to chemical activation, which is also seen to be involved in the rearrangement of p-, m-, and o-phenylenebiscarbenes 25–27 to phenylacetylene 12.

Nitrene-Carbene-Carbene Rearrangement. Photolysis and Thermolysis of Tetrazolo[5,1-a]phthalazine with Formation of 1-Phthalazinylnitrene, o-Cyanophenylcarbene, and Phenylcyanocarbene

1-Azidophthalazine 9A is generated in trace amount by mild FVT of tetrazolo[5,1-a]phthalazine 9T and is observable by its absorption at 2121 cm(-1) in the Ar matrix IR spectrum. Ar matrix photolysis of 9T/9A at 254 nm causes ring opening to generate two conformers of (o-cyanophenyl)diazomethane 11 (2079 and 2075 cm(-1)), followed by (o-cyanophenyl)carbene (3)12, cyanocycloheptatetraene 13, and finally cyano(phenyl)carbene (3)14 as evaluated by IR spectroscopy. The two carbenes (3)12 and (3)14 were observed by ESR spectroscopy (D|hc = 0.5078, E|hc = 0.0236 and D|hc = 0.6488, E|hc = 0.0195 cm(-1), respectively). The rearrangement of 12 ⇄ 13 ⇄ 14 constitutes a carbene-carbene rearrangement. 1-Phthalazinylnitrene (3)10 is observed by means of its UV-vis spectrum in Ar matrix following FVT of 9 above 550 °C. Rearrangement to cyanophenylcarbenes also takes place on FVT of 9 as evidenced by observation of the products of ring contraction, viz., fulvenallenes and ethynylcyclopentadienes 16-18. Thus the overall rearrangement 10 → 11 → 12 ⇄ 13 ⇄ 14 can be formulated.

FTIR spectra and density functional theory P.E.D. assignments of oxiranes in Ar matrix at 12 K

The FTIR spectra of a series of oxiranes were studied in Ar matrix at 12K. The interpretation of the spectra was accomplished on the basis of density functional theory calculations employing the 6-311++G(3df,3pd) basis set with the B3LYP functional. Potential energy distribution was carried out for each molecule employing the B3LYP/6-311++G(3df,3pd) force field and a non-redundant definition of internal coordinates. The study of the FTIR spectra led to the reassignment of some vibrational modes of the molecules. The FTIR spectrum of trifluoroepoxypropane measured in Ar matrix and its assignment is reported for the first time.

Matrix Isolation and Computational Study of the [H, C, N, Se] Isomers

Nine minima on the ground-state singlet and ten minima on the lowest-energy triplet potential energy surfaces of the [H, C, N, Se] system were located at the B3LYP/aug-cc-pVTZ level of theory. The singlet isomers were further investigated by the higher-level CCSD(T) method. Besides their structure and relative energies, isomerization barriers and the dissociation energies of the most important fragmentation channels were determined. Anharmonic vibrational wavenumbers, infrared intensities, relative Raman intensities, and UV excitation energies were also computed to assist the detection of these species. Two of the singlet isomers were generated and investigated by IR and UV spectroscopic methods. First, HNCSe and its deuterated isotopomer, DNCSe, were prepared by the reaction of HBr/DBr with AgNCSe and deposited in an 8 K Ar matrix. Photolysis of (H/D)NCSe at 254 nm led to the formation of the novel (H/D)SeNC isomer, which decomposed upon broad-band UV irradiation.

Theoretical study of the electronic excitations of free-base porphyrin–Ar2 van der Waals complexes

The intermolecular interaction of free-base porphine (FBP)-Ar2 and free-base tetraazaporphyrin (FBPz)-Ar2 van der Waals (vdW) complexes was calculated in the ground state and vertical excitations that correspond to the Q- and B-bands using the many-body wavefunction theory of the symmetry-adapted cluster-configuration interaction (SAC-CI) method and time-dependent density functional theory (TDDFT). For the 1(1)B3u state of FBP-Ar2 a blueshift (high-energy shift) of excitation energy was calculated using the SAC-CI method; such a blueshift was not obtained by TDDFT calculations. This calculated blueshift corresponds to the experimentally observed blueshift in the Qx-band of FBP for FBP-Arn complexes. For FBPz-Ar2, blueshifts of the Q-band were not obtained using SAC-CI and TDDFT. These behaviors of the energy shift of the Q-bands could not be explained by the point dipole-point dipole interaction model. Large redshifts (low-energy shift) were obtained for the B-band states (2(1)B3u and 2(1)B2u) of FBP and FBPz. The energy shift showed the inverse sixth-power dependence on the intermolecular distance. The point dipole-point dipole interaction model can describe the redshift of the B-band. For the excited states that exhibit large redshifts, the TDDFT can qualitatively describe the vdW interaction in the excited states by supermolecular calculations. The solvatochromic shifts for FBP and FBPz in an Ar matrix were examined by the linear-response polarizable continuum model and TDDFT. The magnitude of calculated solvatochromic redshifts is proportional to the square of the transition dipole moment.

Chlorodifluoroacetyl Isothiocyanate, ClF2CC(O)NCS: Preparation and Structural and Spectroscopic Studies

Chlorodifluoroacetyl isothiocyanate, ClF2CC(O)NCS, was synthesized by the reaction of ClF2CC(O)Cl with an excess of AgNCS. The colorless product melts at -85 °C, and its vapor pressure follows the equation ln p = -4471.1 (1/T) + 11.35 (p [atm], T [K]) in the range -38 to 22 °C. The compound has been characterized by IR (gas phase, Ar matrix, and matrix photochemistry), by liquid Raman, by (19)F and (13)C NMR, gas UV-vis, and photoelectron spectroscopy (PES), by photoionization mass spectrometry (PIMS), and by gas electron diffraction (GED). The conformational properties of ClF2CC(O)NCS have been analyzed by joint application of vibrational spectroscopy, GED and quantum chemical calculations. The existence of two conformers has been detected in the gas and liquid phases, in which the C-Cl bond adopts a gauche orientation with respect to the C═O group; the C═O group is in syn- or anti-position with respect to the N═C double bond of the NCS group. The computed ΔG° difference between these two gauche-syn and gauche-anti forms is ΔG° = 0.63 kcal mol(-1) in the B3LYP/6-31G(d) approximation. The most significant gas-phase structural parameters for gauche-syn ClF2CC(O)NCS are re(NC═S) 1.559(2) Å, re(N═CS) 1.213(2) Å, re(N-C) 1.399(7) Å, re(C═O) 1.199(2) Å, and ∠e(CNC) 134.7(13)°. Photolysis of ClF2CC(O)NCS using an ArF excimer laser (193 nm) mainly yields ClF2CNCS, CO, and ClC(O)CF2NCS. The valence electronic properties of the title compound were studied using PES and PIMS. The experimental first vertical ionization energy of 10.43 eV corresponds to the ejection primarily of the sulfur lone-pair electrons of the in-plane nonbonding orbital on the NCS group.

Complexes of acetylene–fluoroform: A matrix isolation and computational study

Hydrogen-bonded complexes of C2H2 and CHF3 have been investigated using matrix isolation infrared spectroscopy and ab initio computations. The complexes were trapped in both solid argon and nitrogen matrices at 12K. The structure of the complexes and the energies were computed at the B3LYP and MP2 levels of theory using a 6-311++G(d,p) basis set and at the MP2/aug-cc-pvdz level. Our computations indicated two minima for the 1:1 C2H2–CHF3 complex, with the C–H…π complex being the global minimum, where CHF3 is the proton donor. The second minimum corresponded to a relatively less exothermic C–H…F complex, in which C2H2 is the proton donor. Experimentally, we observed only the C–H…π complex in our matrix, which was evidenced by the shifts in the vibrational frequencies of the modes involving the C2H2 and CHF3 sub-molecules. The increase in the blue shift of the C–H stretching frequency in going from CHCl3–acetylene complex to CHF3–acetylene complex with corresponding increase in the interaction energy helps to place these two complexes on the left hand end of the qualitative diagram (Fig. 1). We also performed computations to study the higher complexes of C2H2 and CHF3. One minimum was found for the 1:2 C2H2–CHF3 complexes and two minima for the 2:1 C2H2–CHF3 complexes, at all levels of theory. Experimentally we observed the features corresponding to the 1:2 and 2:1 C2H2–CHF3 complexes in the N2 matrix. The computed vibrational frequencies of C2H2–CHF3 complexes at B3LYP and MP2/6-311++G(d,p) level corroborated well with the experimental frequencies. Interestingly, no experimental evidence for the formation of higher complexes was observed in the Ar matrix.

Matrix Isolation Spectroscopy and Nuclear Spin Conversion of NH3 and ND3 in Solid Parahydrogen

We present matrix isolation infrared absorption spectra of NH3 and ND3 trapped in solid parahydrogen (pH2) at temperatures around 1.8 K. We used the relatively slow nuclear spin conversion (NSC) of NH3 and ND3 in freshly deposited pH2 samples as a tool to assign the sparse vibration-inversion-rotation (VIR) spectra of NH3 in the regions of the ν2, ν4, 2ν4, ν1, and ν3 bands and ND3 in the regions of the ν2, ν4, ν1, and ν3 fundamentals. Partial assignments are also presented for various combination bands of NH3. Detailed analysis of the ν2 bands of NH3 and ND3 indicates that both isotopomers are nearly free rotors; that the vibrational energy is blue-shifted by 1-2%; and that the rotational constants and inversion tunneling splitting are 91-94% and 67-75%, respectively, of the gas-phase values. The line shapes of the VIR absorptions are narrow (0.2-0.4 cm(-1)) for upper states that cannot rotationally relax and broad (>1 cm(-1)) for upper states that can rotationally relax. We report and assign a number of NH3-induced infrared absorption features of the pH2 host near 4150 cm(-1), along with a cooperative transition that involves simultaneous vibrational excitation of a pH2 molecule and rotation-inversion excitation of NH3. The NSCs of NH3 and ND3 were found to follow first-order kinetics with rate constants at 1.8 K of k = 1.88(16) × 10(-3) s(-1) and k = 1.08(8) × 10(-3) s(-1), respectively. These measured rate constants are compared to previous measurements for NH3 in an Ar matrix and with the rate constants measured for other dopant molecules isolated in solid pH2.

High-Resolution Rovibrational Spectroscopy of Jet-Cooled Phenyl Radical: The ν19 Out-of-Phase Symmetric CH Stretch

Phenyl radical has been studied via sub-Doppler infrared spectroscopy in a slit supersonic discharge expansion source, with assignments for the highest frequency b2 out-of-phase C-H symmetric stretch vibration (ν19) unambiguously confirmed by ≤6 MHz (0.0002 cm(-1)) agreement with microwave ground state combination differences of McMahon et al. [Astrophys. J. 2003, 590, L61-64]. Least squares analysis of over 100 resolved rovibrational peaks in the sub-Doppler spectrum to a Watson Hamiltonian yields precision excited-state rotational constants and a vibrational band origin (ν0 = 3071.8915(4) cm(-1)) consistent with a surprisingly small red-shift (0.9 cm(-1)) with respect to Ar matrix isolation studies of Ellison and co-workers [J. Am. Chem. Soc. 2001, 123, 1977]. Nuclear spin weights and inertial defects confirm the vibrationally averaged planarity and (2)A1 rovibronic symmetry of phenyl radical, with analysis of the rotational constants consistent with a modest C2v distortion of the carbon backbone frame due to partial sp rehybridization of the σ C radical-center. Most importantly, despite the number of atoms (N = 11) and vibrational modes (3N - 6 = 27), phenyl radical exhibits a remarkably clean jet cooled high-resolution IR spectrum that shows no evidence of intramolecular vibrational relaxation (IVR) phenomena such as local or nonlocal perturbations due to strongly coupled nearby dark states. This provides strong support for the feasibility of high-resolution infrared spectroscopy in other aromatic hydrocarbon radical systems.

The biomolecule of 5-bromocytosine: FT-IR and FT-Raman spectra and DFT calculations. Identification of the tautomers in the isolated state and simulation the spectra in the solid state

An accurate assignment of the IR spectrum in Ar matrix of 5-bromocytosine and of the IR and Raman spectra in the solid state was carried out. For this purpose Density functional calculations (DFTs) were performed to clarify wavenumber assignments of the experimental observed bands. The calculated values were scaled using scaling equations and they were compared with IR and Raman experimental data. Good reproduction of the experimental wavenumbers is obtained and the% error is very small in the majority of cases. In the isolated state all the tautomer forms of 5-bromocytosine were determined and optimized. The wavenumbers corresponding to C1 and C2b tautomers were identified and assigned in the IR experimental spectrum reported in Ar matrix. Our study confirms the existence of at least two tautomers, the amino-oxo and the amino-hydroxy in the isolated state.In the solid state the FT-IR and FT-Raman spectra of 5-bromocytosine in the powder form were recorded in the region 400–4000cm−1 and 50–3500cm−1, respectively. The unit cell found in the crystal was simulated as a tetramer form in three tautomers. Thus, it has been possible to assign all the 33 normal modes of vibration. The study indicates that the features, that are the characteristic of the vibrational spectra of cytosine, are retained by the spectra of 5-bromocytosine and it exists in the solid phase in the amino-oxo form.

Simulation of a tetramer form of 5-chlorouracil: The vibrational spectra and molecular structure in the isolated and in the solid state by using DFT calculations

A Raman and FT-IR study of the biomolecule 5-chlorouracil in the solid state was carried out. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify the assignments of the experimentally observed bands in the spectra. Calculations in the monomer form and comparisons with the experimental data in Ar matrix were also carried out. The error in the calculated frequencies was analyzed and reduced by using scaling equations and scaling factors deduced from the uracil molecule. The calculations with the B3LYP method and with the 6-31G(d,p) and 6-311+G(2d,p) basis set, appear in general to be useful, when combining with a scaling equation procedure or with the specific scale factors, for interpretation of the general features of the IR and Raman spectra. The scaled values were used in the reassignment of the IR and Raman experimental bands. Comparison of the results with those determined in uracil and 5-halogenated derivatives were performed. The substitution at 5-position of the uracil ring by a chlorine atom has a little effect on the geometric parameters.