The attachment of amino fragment to purine: inner‐shell structures and spectra

The impact of the amino fragment (–NH₂) attachment on the inner‐shell structures and spectra of unsubstituted purine and the purine ring of adenine are studied. Density functional theory calculations, using the LB94/TZ2P//B3LYP/TZVP model, reveal significant site‐dependent electronic structural changes in the inner shell of the species. A condensed Fukui function indicates that all of the N and C sites, except for N₍₁₎ and C₍₅₎, demonstrate significant electrophilic reactivity (f^? > 0.5 in |e|) in the unsubstituted purine. Once the amino fragment binds to the C₍₆₎ position of purine to form adenine, the electrophilic reactivity of these N and C sites is greatly reduced. As expected, the C₍₆₎ position experiences substantial changes in energy and charge transfer, owing to the formation of the C—NH₂ bond in adenine. The present study reveals that the N1s spectra of adenine inherit the N1s spectra of the unsubstituted purine, whereas the C1s spectra experience significant changes although purine and adenine have geometrically similar carbon frames. The findings also indicate that the attachment of the NH₂ fragment to purine exhibits deeply rooted influences to the inner‐shell structures of DNA/RNA bases. The present study suggests that some fragment‐based methods may not be applicable to spectral analyses in the inner shell.     

Impact of ketone and amino on the inner shell of guanine

Removal of the functional groups of guanine, i.e. ketone and amino, one by one produces model molecules of hypoxanthine, 2‐aminopurine and unsubstituted purine. The impact of the ketone and amino moieties on guanine is revealed using their atomic‐site‐based inner‐shell electronic properties and spectra. A density functional theory based model has been employed to study the model molecules. Electronic properties, such as Hirshfeld charges and inner‐shell chemical shift, are found to be both site‐dependent and moiety‐dependent. The site‐based inner‐shell chemical shift of the species exhibits a simple linear correlation, although certain similarities among the model molecules regroup the species into two pairs of purine and 2‐aminopurine, as well as hypoxanthine and guanine.     

Introducing boranorcaradienes with more stability than their corresponding borepins: Reversal of tautomerization via substituents at theoretical levels

In contrast to typical borepins, which appear about 40.0 kcalmol^?1 more stable than their corresponding tautomeric boranorcaradienes, we have found 2 species, which have reversed this trend and pushed the equilibrium in favor of their corresponding boranorcaradienes. They are namely 1a,9b‐dihydro‐1H‐borireno[2,3‐h]pyridazino[4,3‐f]cinnoline and 1a,9b‐dihydro‐1H‐borireno[2,3‐h]pyrimido[5,4‐f]quinazoline which stand up among 14 isomeric systems probed, at B3LYP/AUG‐cc‐pVTZ, M06‐2X/AUG‐cc‐pVTZ, MP2/AUG‐cc‐pVTZ, and HF/AUG‐cc‐pVTZ. Energy barriers are calculated in gas‐phase, where the possibility of a rapid interconversion of the isomers is ruled out. Generally, dibenzoboranorcaradienes assume C_s symmetry with planar geometry and dihedral angle of zero degree. In contrast, their corresponding borepins show a high tendency for puckering with dihedral angle of ~66°. The preference of the latter for puckered non‐planar geometries is evidenced by natural bonding orbitals calculations and visually through their frontier molecular orbitals. Main interactions appear to be hyperconjugations of σ and π bonds across the rings. Position and number of nitrogen atoms on the fused rings seem to affect the energy gap, dipole moment, symmetry, dihedral angle, the chemical shift, NICS, bond lengths, and charge distribution.     

The resonance and pre‐resonance Raman scattering in the low energy 11B2u and 11B3u states of 1,4,5,8‐naphthalenetetracarboxy dianhydride in terms of DFT methods. The aggregation of NTCDA molecules in the ethanol and methanol solutions

The absorption, pre‐resonance, and resonance Raman spectra of 1,4,5,8‐naphthalenetetracarboxy dianhydride (NTCDA) molecule are examined in terms of time‐dependent density functional theory at TD‐B3LYP/aug‐cc‐pVDZ and TD‐SVWN/aug‐cc‐pVDZ levels. The Franck–Condon analysis performed for two 1¹A_g → 1¹B_2u and 1¹A_g → 1¹B_3u overlapping transitions leads to an excellent agreement between the theoretical predictions and experimental data providing that the calculated absorption is confronted with that measured in chloroform or acetonitrile but not in the ethanol (methanol) solution. We argue that absorption spectra measured in ethanol solution already known in literature do not characterize NTCDA molecule. On the basis of the absorption and resonance scattering spectra, we may deliberate that the dimerization of NTCDA is responsible for utterly different absorption observed in ethanol (methanol) comparing with less active solvents (chloroform and acetonitrile). That conclusion is supported by the dimer vibronic theory and by the TD‐B97d computations at the aug‐cc‐pVDZ basis set level. Copyright © 2013 John Wiley & Sons, Ltd.     

A combined quantum mechanical and experimental approach towards chiral diketopiperazine hydroperoxides

In order to improve hydroperoxide formation from heterocyclic compounds relating to the formation rate and to allow a suitable choice of starting materials for autoxidation, theoretical studies on a set of different amino acid‐derived diketopiperazines and pyrazinoquinazolines were carried out. To estimate their reactivity towards hydroperoxide formation, bond dissociation enthalpies (BDEs) of tertiary α‐C? H bonds as well as reaction enthalpies to the corresponding hydroperoxides were calculated at the B3LYP/TZVP and RMP2/aug‐cc‐pVTZ level of theory. The Evans–Polanyi relation was then used to correlate substrate reactivity with calculated BDEs. Thermal and zero point vibrational energy (ZPE) corrections were determined in the classical harmonic oscillator‐rigid rotor‐particle in a box model. While for the investigated set of diketopiperazines BDEs of 318.8–327.0 kJ mol^?1 were found, BDEs for pyrazinoquinazolines spread between 248.4 and 368.4 kJ mol^?1 at the B3LYP/TZVP level of theory. A selected subset of heterocycles was converted to the corresponding hydroperoxides and the diketopiperazines were obtained in up to 39% yield after 5–7 days, whereas the pyrazinoquinazoline hydroperoxides were isolated in up to 67% yield after 24 h. Thus, replacing an amido moiety in an N‐aryl‐imino moiety when using pyrazinoquinazolines instead of diketopiperazines leads indeed to an improved captodative stabilization of the radical intermediate. Furthermore the theoretical calculations allowed a distinctive forecast of the preferred regioisomeric hydroperoxide. Copyright © 2010 John Wiley & Sons, Ltd.     

Correlation of methane Raman ν1 band position with fluid density and interactions at the molecular level

The CH₄ Raman ν₁ symmetric stretching band position was measured at various temperatures and pressures over the range 1–600 bars and 0.3–22 °C. The ν₁ symmetric stretching band shifts to lower wavenumbers with increasing pressure and/or decreasing temperature, and shows a systematic correlation with density over this same range. Ab initio calculations (MP2/aug‐cc‐pVTZ) show that the changes in peak shape and position reflect fundamental distortion of the methane structure as the density increases. Copyright © 2007 John Wiley & Sons, Ltd.     

Structural and energetic properties of alkylfluoride–BF3 complexes in the gas phase and condensed‐phase media: computations and matrix infrared spectroscopy

We have undertaken an experimental and computational study of the structural properties of a few alkylfluoride–BF₃ complexes (RF′–BF₃), which are proposed intermediates in a certain class of Friedel–Crafts reactions. Using density functional theory and second‐order Møller–Plesset calculations, we have obtained gas‐phase structures, frequencies, and B–F′ bond potentials for CH₃F–BF₃, (CH₃)₂CHF–BF₃, and (CH₃)₃CF–BF₃. All the complexes are weakly‐bonded in the gas phase, with B–F′ distances (X3LYP/aug‐cc‐pVTZ) of about 2.4 Å and binding energies (MP2/aug‐cc‐pVTZ) ranging from 5.4 and 6.7 kcal/mol. Accordingly, gas‐phase bond potentials are relatively shallow and flat for these complexes. However, even though the inner walls of the potentials are rather soft (the energies rise by only about 5 to 10 kcal/mol between 2.4 and 1.6 Å), we observe no global or local minima at short B–F′ distances. For the (CH₃)₂CHF–BF₃ and (CH₃)₃CF–BF₃ potentials in dielectric media, we do observe a distinct flattening along the inner wall, which results in shelf‐like region near 1.7 Å, but this feature is not a true local minimum. We have also obtained low‐temperature infrared spectra of the (CH₃)₂CHF–BF₃ complex in solid neon, and the frequencies agree quite favorably with those obtained via computations, which validates the computational assessment of the gas‐phase complexes. Copyright © 2011 John Wiley & Sons, Ltd.     

A vibrational spectroscopic investigation of rhodanine and its derivatives in the solid state

Raman and infrared spectra are reported for rhodanine, 3‐aminorhodanine and 3‐methylrhodanine in the solid state. Comparisons of the spectra of non‐deuterated/deuterated species facilitate discrimination of the bands associated with N H, NH₂, CH₂ and CH₃ vibrations. DFT calculations of structures and vibrational spectra of isolated gas‐phase molecules, at the B3‐LYP/cc‐pVTZ and B3‐PW91/cc‐pVTZ level, enable normal coordinate analyses in terms of potential energy distributions for each vibrational normal mode. The cis amide I mode of rhodanine is associated with bands at ∼1713 and 1779 cm⁻¹, whereas a Raman and IR band at ∼1457 cm⁻¹ is assigned to the amide II mode. The thioamide II and III modes of rhodanine, 3‐aminorhodanine and 3‐methylrhodanine are observed at 1176 and 1066/1078; 1158 and 1044; 1107 and 984 cm⁻¹ in the Raman and at 1187 and 1083; 1179 and 1074; 1116 and 983 cm⁻¹ in the IR spectra, respectively. Copyright © 2010 John Wiley & Sons, Ltd.     

Hydrogen bond and internal rotations barrier: DFT study on heavier group‐14 analogues of formamide

A theoretical study on heavier group‐14 substituting effect on the essential property of formamide, strong hydrogen bond with water and internal rotational barrier was performed within the framework of natural bond orbital (NBO) analysis and based on the density functional theory calculation. For heavier group‐14 analogues of formamide (YHONH₂, Y = Si, Ge and Sn), the n_N–π_Y=O conjugation strength does not always reduce as Y becomes heavier, for example, silaformamide and germaformamide have similar strength of delocalization. Heavier formamides prefer being H‐bond donors to form FYO–H₂O complexes to being H‐bond acceptors to form FYH–H₂O complexes. The NEDA analysis indicates that H‐bond energies of FYO–H₂O complexes increase as moving down group 14 due to concurrently stronger charge transfer (CT) and electrostatic attraction and for the FYH–H₂O complexes H‐bond strengths are similar. The model of CTs from FYO to H₂O differs from that at FYH–H₂O complexes, which are contributed not only by aligning lone‐pair orbital of O but also by another lone‐pair orbital. At two lowest lying excited states (the triplet and S₁ excited states), formamide and its heavier analogues form double H‐bonds with H₂O molecule at the same time. The barrier heights of internal rotation become gradually low from C to Sn, formamide (15.73 kcal/mol) > silaformamide (11.73 kcal/mol) > germaformamide (9.45 kcal/mol) > stannaformamide (7.50 kcal/mol) at the CCSD(T)/aug‐cc‐pVTZ//B3LYP/cc‐pVTZ level. NBO analysis indicates that the barrier does not only come from the n_N→π*_YO conjugation, and for heavier analogues of formamide, the n_N→σ*_YO hyperconjugation effect and steric effect considerably contribute to the overall rotational barrier. Copyright © 2013 John Wiley & Sons, Ltd.     

Effects of alkyl side chains on properties of aliphatic amino acids probed using quantum chemical calculations

Effects of alkyl side chains (R‐) on the electronic structural properties of aliphatic amino acids are investigated using quantum mechanical approaches. The carbon (C 1s) binding energy spectra of the aliphatic amino acids are derived from the C 1s spectrum of glycine (the parent spectrum) by the addition of spectral peaks, depending on the alkyl side chains, appearing in the lower energy region IP < 290 eV (where IP is the ionization potential). The two glycyl parent spectral peaks of the amide 291.0 eV [C₍₂₎] and carboxylic 293.5 eV [C₍₁₎] C atoms are shifted in the aliphatic amino acids owing to perturbations depending on the size and structure of the alkyl chains. The pattern of the N 1s and O 1s spectra in glycine is retained in the spectra of the other amino acids with small shifts to lower energy, again depending on the alkyl side chain. The Hirshfeld charge analyses confirm the observations. The alkyl effects on the valence binding energy spectra of the amino acids are concentrated in the middle valence energy region of 12–16 eV, and hence this energy region of 12–16 eV is considered as the `fingerprint' of the alkyl side chains. Selected valence orbitals, either inside or outside of the alkyl fingerprint region, are presented using both density distributions and orbital momentum distributions, in order to understand the chemical bonding of the amino acids. It is also observed that the HOMO–LUMO energy gaps of the aliphatic amino acids are reduced with the growth of the alkyl side chain.     

An experimental and computational study of the valence photoelectron spectra of halogenated pyrimidines

The electronic structures of pyrimidine and a selection of its halogen-substituted derivatives have been investigated using ultraviolet photoelectron spectroscopy and ab initio quantum chemical methods. Assignments are proposed for all of the features in the PES spectra by comparison with the vertical ionization energies of the molecular orbitals calculated using the partial third-order quasiparticle approximation as applied to electron propagator theory and a corrected density functional method based on the B3LYP functional. The shifts of the outermost five molecular orbitals of the pyrimidine ring structure in the halogen-substituted derivatives with respect to the binding energies of the equivalent orbitals in the parent pyrimidine molecule are discussed as a function of the identity and ring position of the halogen atom.     

Vibrational spectroscopy and DFT calculations of N,N′‐dicyclohexylcarbodiimide

Infrared (IR) and Raman spectra were obtained for N,N′‐dicyclohexylcarbodiimide (DCC) in the solid state and in CHCl₃ solution. Structures and vibrational spectra of isolated, gas‐phase DCC molecules with C₂ and C_i symmetries, computed at the B3‐LYP/cc‐pVTZ level, show that the IR and Raman spectra provide convincing evidence for a C₂ structure in both the solid state and in CHCl₃ solution. Using a scaled quantum‐chemical force field, these density functional theory calculations have provided detailed assignments of the observed IR and Raman bands in terms of potential energy distributions. Comparison of solid‐state and solution spectra, together with a Raman study of the melting behaviour of DCC, revealed that no solid‐state effects were evident in the spectra. Copyright © 2010 John Wiley & Sons, Ltd.     

P‐Heterocyclic silylenes: a survey of stability with density functional theory

The effects of phosphorous atom on the stability, multiplicity, and reactivity of six‐member cyclic silylenes are investigated at B3LYP/AUG‐cc‐pVTZ//B3LYP/6‐31+G* and MP2/6‐311++G**//B3LYP/6‐31+G* coupled with appropriate isodesmic reactions. From a thermodynamic point of view, 1H‐2‐silaphosphinine‐2‐ylidene ( 1_a ) and 1H‐4‐silaphosphinine‐4‐ylidene ( 2_a ) are relatively the most stable with singlet–triplet energy gaps (ΔE_S–T) of 37.0 and 28.1 kcal/mol, respectively. The calculated energy barrier for the 1,2‐H shift of 1_a to the corresponding 2‐silapyridine ( 1 ) is 26.5 kcal/mol, which is lower than the 28.8 kcal/mol required for the 1,4‐H shift of 2_a to the corresponding 4‐silapyridine ( 2 ). In contrast to the previous reports, isodesmic reactions indicate that π‐donor/σ‐donor phosphorous destabilizes the singlet while stabilizes the triplet state. Both 1_a and 2_a silylenes appear invulnerable to the head‐to‐head as well as the head‐to‐tail dimerization, inviting experimental explorations. Copyright © 2011 John Wiley & Sons, Ltd.     

Conformational,vibrational, and structural studies of 2,2,3,3,3‐pentafluoropropylamine from Raman and infrared spectra of gas,liquid, xenon solutions,and solid supported by ab initio calculations

The Raman and infrared spectra (3500–50 cm⁻¹) of the gas, liquid or solution, and solid were recorded of 2,2,3,3,3‐pentafluoropropylamine (CF₃CF₂CH₂NH₂) and the ND₂ isotopomer. Variable temperature (−55 to − 100 °C) studies of the infrared spectra (3600–400 cm⁻¹) of samples dissolved in liquid xenon have been carried out. From these data, two of the five possible conformers have been identified and their relative stabilities obtained. The enthalpy difference was determined between the more stable Tt conformer and the less stable Tg form to be 280 ± 14 cm⁻¹ (3.35 ± 0.17 kJ/mol). The first indicator is the NCCC dihedral angle (G = gauche or T = trans), and the second one (g = gauche or t = trans) is the relative position of the lone pair of electrons on nitrogen with respect to the β‐carbon. The percentage of the Tg conformer at ambient temperature is estimated to be 34 ± 2%. The conformational stabilities have been predicted from ab initio calculations utilizing several different basis sets up to aug‐cc‐pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for most of the observed bands for both isotopomers, supported by MP2(full)/6‐31G(d) ab initio calculations to predict the harmonic force fields, wavenumbers, infrared intensities, Raman activities, and depolarization ratios for both conformers. Estimated r₀ structural parameters were obtained from adjusted MP2(full)/6‐311 + G(d,p) calculations. The results are discussed and compared with the corresponding properties of some related molecules. Copyright © 2011 John Wiley & Sons, Ltd.     

A theoretical investigation into dimethylcarbene and its diamino and diphosphino analogs: effects of cyclization and unsaturation on the stability and multiplicity

High levels of ab initio and DFT calculations (B3LYP/6‐311++G**, B3LYP/AUG‐cc‐pVTZ, and CCSD(T)/6‐311++G** levels) coupled with isodesmic reactions are used to compare and contrast the multiplicities and relative stabilities of singlet (s) and triplet (t) acyclic carbenes, including: dimethylcarbene, diaminocarbene, and diphosphinocarbene along with their saturated and unsaturated cyclic ones. Cyclization is unfavorable for all acyclic carbenes while unsaturation of cyclic analogs appears favorable. The simultaneous cyclization and unsaturation of dimethylcarbene increases the singlet–triplet energy gap (ΔE_s–t), while for diphosphinocarbene the situation is reversed. For diaminocarbene the increase of ΔE_s–t is encountered only during cyclization. Copyright © 2009 John Wiley & Sons, Ltd.     

Inner shell excitation,valence excitation and core ionization in NF3 studied by electron energy-loss and X-ray photoelectron spectroscopies

Electron energy-loss Spectroscopy (EELS) at impact energies of 2.5–3 keV has been used to obtain the electron excitation spectra for the N 1s (K-shell), F 1s (K-shell) and valence shell regions of NF₃. The inner shell spectra were recorded using small angle scattering (?1° ) while the valence shell spectrum was obtained at zero degree scattering angle. The inner shell excitation spectra show a strongly enhanced 1s→ δ^* type transition and continuum features which are typical for molecules with highly electronegative ligands. One of the peaks in an earlier published photoabsorption study of the N 1s region has been shown to be due to a N₂ impurity. The valence shell electron energy-loss spectrum shows a number of transitions which are considered to be mainly due to valence-valence type transitions, with also some evidence of Rydberg structure.The X-ray photoelectron spectra (XPS) of the N 1s and F 1s electrons along with their associated satellite structures have also been recorded using Al Kα (1486.58 eV) radiation. The vertical ionization potentials for the N 1s and F 1s electrons were found to be 414.36 (10) eV and 693.24 (10) eV, respectively. Both spectra exhibit a rich and different satellite structure. These “shake-up” features in the satellite XPS spectra are compared with continuum features of the inner shell electron energy-loss spectra and also with the valence shell spectrum.     

Effects of α‐cyclopropyl on heterocyclic carbenes stability at DFT

α‐Cyclopropyl stability impacts on singlet and triplet heterocyclic carbenes with acyclic, cyclic, and cyclic‐unsaturated structures are compared and contrasted to di‐t‐butyl as well as t‐butylcyclopropylcarbenes through appropriate isodesmic reactions at B3LYP/AUG‐cc‐pVTZ level. Substitution of one of the t‐butyl groups of di‐t‐butylcarbene with a cyclopropyl alters the ground state multiplicity from triplet to singlet with a singlet–triplet energy separation (ΔE_s–t) of 7.2 kcal/mol. Additional heteroatom substitution increases ΔE_s–t values for the resulting α‐heteroatom cyclopropylcarbenes in the following order: amino > oxy > thio > phophino. α‐Cyclopropyl group stabilizes singlet states of all our carbenes two to three times more than their corresponding triplet states. The ΔE_s–t values of all the carbenes are increased through cyclization, while the introduction of unsaturation in the rings causes small and rather random changes. To probe the kinetic stability of the species, we calculated the transition states for the opening of cyclopropyl through 1,2‐C shift. Interestingly, the 4.1 kcal/mol energy barrier in cyclopropylcarbene is significantly increased in the presence of heteroatoms to 31.2 kcal/mol for aminocyclopropylcarbene. The reactivity of the species is discussed in terms of nucleophilicity and electrophilicity issues showing our carbenes, especially acyclic ones, more nucleophilic than the common N‐heterocyclic carbenes. Copyright © 2010 John Wiley & Sons, Ltd.     

Conformational and structural studies of n‐propylamine from temperature dependent Raman and far infrared spectra of xenon solutions and ab initio calculations

The Raman and infrared spectra (4000 to 50 cm^–1) of the gas, liquid or solution, and solid have been recorded of n‐propylamine, CH₃CH₂CH₂NH₂. Variable temperature (−60 to −100 °C) studies of the Raman (1175 to 625 cm^–1) and far infrared (600 to 10 cm^–1) spectra dissolved in liquid xenon were carried out. From these data, the five possible conformers were identified and their relative stabilities obtained with enthalpy difference relative to trans–trans (Tt) for trans–gauche (Tg) of 79 ± 9 cm^–1 (0.9 ± 0.1 kJ/mol); for Gg of 91 ± 26 cm^–1 (1.08 ± 0.3 kJ/mol); for Gg′ of 135 ± 21 cm^–1 (1.61 ± 0.2 kJ/mol); for Gt of 143 ± 11 cm^–1 (1.71 ± 0.1 kJ/mol). The percentage of the five conformers is estimated to be 18% for the Tt, 24 ± 1% for Tg, 23 ± 3% for Gg, 18 ± 1% for Gg′ and 18 ± 1% for Gt at ambient temperature. The conformational stabilities have been predicted from ab initio calculations utilizing several different basis sets up to aug‐cc‐pVTZ from both second‐order Møller–Plesset (MP2, full) and density functional theory calculations by the Becke, three‐parameter, Lee–Yang–Parr method. Vibrational assignments were provided for the observed bands for all five conformers, which are supported by MP2(full)/6‐31G(d) ab initio calculations to predict harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r₀ structural parameters were obtained from adjusted MP2(full)/6‐311+G(d,p) calculations. The results are discussed and compared with the corresponding properties of some related molecules. Copyright © 2012 John Wiley & Sons, Ltd.     

Tobacco alkaloids analyzed by Raman spectroscopy and DFT calculations

The tobacco alkaloids: nicotine, nornicotine, cotinine, anabasine, their protonated forms, and salts were analyzed by means of Raman spectroscopy supported by the density functional theory/B3LYP/aug‐cc‐pVDZ calculations. The analyses were performed based on Raman marker bands of neutral, monoprotonated, and diprotonated forms of tobacco alkaloids because in different surroundings various forms have been suggested to either dominate or to coexist. The form and distribution of nicotine directly in a plant and in phytopharmaceutical products were investigated by in situ Raman mapping. For the first time, the Raman optical activity spectrum of (−)‐nicotine in aqueous solution was measured and interpreted by means of the density functional theory calculations. The study provides a clear evidence that Raman spectroscopy techniques are powerful in efficient quality control and forensic and bioanalytical analyses of tobacco alkaloids. Copyright © 2012 John Wiley & Sons, Ltd.