Competitive Gas Phase Reactions for the Production of Isomers C2O2H4. Spectroscopic Constants of Methyl Formate.

New routes for the chemical formation of the C2O2H4 isomers in the gas phase are explored searching for a justification of the prominent astrophysical abundance of methyl formate with respect to the most stable one acetic acid. Kinetic rate constants at low temperatures are provided for eight barrierless reaction pathways. In addition, the spectroscopic parameters are computed using highly correlated ab initio methods for the main isotopologue of methyl formate and for five monosubstituted isotopologues containing 13C, 18O, and deuterium. Accurate rotational constants are obtained at the CCSD(T)-F12 level of theory. The dipole moments components are provided. Centrifugal distortion constants, rovibrational parameters, and Fermi displacements are predicted using second order perturbation theory. A variational procedure of reduced dimensionality is applied to determine band center positions for transitions corresponding to the large amplitude motions. The COC bending mode is considered explicitly as an independent coordinate to evaluate its resonances with the torsional energies. The effect of resonances is proven as negligible.

Ab initio spectroscopic characterization of the radical CH3OCH2 at low temperatures.

Spectroscopic and structural properties of methoxymethyl radical (CH3OCH2, RDME) are determined using explicitly correlated ab initio methods. This radical of astrophysical and atmospheric relevance has not been fully characterized at low temperatures, which has delayed astrophysical research. We provide rovibrational parameters, excitations to the low energy electronic states, torsional and inversion barriers, and low vibrational energy levels. In the electronic ground state (X2A), which appears "clean" from nonadiabatic effects, the minimum energy structure is an asymmetric geometry whose rotational constants and dipole moment have been determined to be A0 = 46 718.67 MHz, B0 = 10 748.42 MHz, and C0 = 9272.51 MHz, and 1.432D (µA = 0.695D, µB = 1.215D, µC = 0.302D), respectively. A variational procedure has been applied to determine torsion-inversion energy levels. Each level splits into 3 subcomponents (A1/A2 and E) corresponding to the three methyl torsion minima. Although the potential energy surface presents 12 minima, at low temperatures, the infrared band shapes correspond to a surface with only three minima because the top of the inversion Vα barrier at α = 0° (109 cm-1) stands below the zero point vibrational energy and the CH2 torsional barrier is relatively high (∼2000 cm-1). The methyl torsion barrier was computed to be ∼500 cm-1 and produces a splitting of 0.01 cm-1 of the ground vibrational state.

Photodissociation of the CH3O and CH3S radical molecules: an ab initio electronic structure study.

The electronic states and the spin-orbit couplings between them involved in the photodissociation process of the radical molecules CH3X, CH3X → CH3 + X (X = O, S), taking place after the Ã(2A1) ← X[combining tilde](2E) transition, have been investigated using highly correlated ab initio techniques. A two-dimensional representation of both the potential-energy surfaces (PESs) and the couplings is generated. This description includes the C-X dissociative mode and the CH3 umbrella mode. Spin-orbit effects are found to play a relevant role in the shape of the excited state potential-energy surfaces, particularly in the CH3S case where the spin-orbit couplings are more than twice more intense than in CH3O. The potential surfaces and couplings reported here for the present set of electronic states allow for the first complete description of the above photodissociation process. The different photodissociation mechanisms are analyzed and discussed in light of the results obtained.

An ab initio study of the ground and excited electronic states of the methyl radical.

The ground and some excited electronic states of the methyl radical have been characterized by means of highly correlated ab intio techniques. The specific excited states investigated are those involved in the dissociation of the radical, namely the 3s and 3pz Rydberg states, and the A1 and B1 valence states crossing them, respectively. The C-H dissociative coordinate and the HCH bending angle were considered in order to generate the first two-dimensional ab initio representation of the potential surfaces of the above electronic states of CH3, along with the nonadiabatic couplings between them. Spectroscopic constants and frequencies calculated for the ground and bound excited states agree well with most of the available experimental data. Implications of the shape of the excited potential surfaces and couplings for the dissociation pathways of CH3 are discussed in the light of recent experimental results for dissociation from low-lying vibrational states of CH3. Based on the ab initio data some predictions are made regarding methyl photodissociation from higher initial vibrational states.

Structural and spectroscopic characterization of methyl isocyanate, methyl cyanate, methyl fulminate, and acetonitrile N-oxide using highly correlated ab initio methods.

Various astrophysical relevant molecules obeying the empirical formula C2H3NO are characterized using explicitly correlated coupled cluster methods (CCSD(T)-F12). Rotational and rovibrational parameters are provided for four isomers: methyl isocyanate (CH3NCO), methyl cyanate (CH3OCN), methyl fulminate (CH3ONC), and acetonitrile N-oxide (CH3CNO). A CH3CON transition state is inspected. A variational procedure is employed to explore the far infrared region because some species present non-rigidity. Second order perturbation theory is used for the determination of anharmonic frequencies, rovibrational constants, and to predict Fermi resonances. Three species, methyl cyanate, methyl fulminate, and CH3CON, show a unique methyl torsion hindered by energy barriers. In methyl isocyanate, the methyl group barrier is so low that the internal top can be considered a free rotor. On the other hand, acetonitrile N-oxide presents a linear skeleton, C3v symmetry, and free internal rotation. Its equilibrium geometry depends strongly on electron correlation. The remaining isomers present a bend skeleton. Divergences between theoretical rotational constants and previous parameters fitted from observed lines for methyl isocyanate are discussed on the basis of the relevant rovibrational interaction and the quasi-linearity of the molecular skeleton.

Weak intramolecular interaction effects on the torsional spectra of ethylene glycol, an astrophysical species.

An elaborate variational procedure of reduced dimensionality based on explicitly correlated coupled clusters calculations is applied to understand the far infrared spectrum of ethylene-glycol, an astrophysical species. This molecule can be classified in the double molecular symmetry group G8 and displays nine stable conformers, gauche and trans. In the gauche region, the effect of the potential energy surface anisotropy due to the formation of intramolecular hydrogen bonds is relevant. For the primary conformer, stabilized by a hydrogen bond, the ground vibrational state rotational constants are computed to be A0 = 15 369.57 MHz, B0 = 5579.87 MHz, and C0 = 4610.02 MHz corresponding to differences of 6.3 MHz, 7.2 MHz, and 3.5 MHz from the experimental parameters. Ethylene glycol displays very low torsional energy levels whose classification is not straightforward and requires a detailed analysis of the torsional wavefunctions. Tunneling splittings are significant and unpredictable due to the anisotropy of the potential energy surface PES. The ground vibrational state splits into 16 sublevels separated ∼142 cm(-1). The splitting of the "G1 sublevels" was calculated to be ∼0.26 cm(-1) in very good agreement with the experimental data (0.2 cm(-1) = 6.95 MHz). Transitions corresponding to the three internal rotation modes allow assignment of previously observed Q branches. Band patterns, calculated between 362.3 cm(-1) and 375.2 cm(-1), 504 cm(-1) and 517 cm(-1), and 223.3 cm(-1) and 224.1 cm(-1), that correspond to the tunnelling components of the v21 fundamental (v21 = OH-torsional mode), are assigned to the prominent experimental Q branches.

Theoretical Spectroscopic Characterization at Low Temperatures of Dimethyl Sulfoxide: The Role of Anharmonicity.

The structural and spectroscopic parameters of dimethyl sulfoxide (DMSO) are predicted from CCSD(T)-F12 calculations that can help to resolve the outstanding problem of the rovibrational spectroscopy. DMSO is a near oblate top that presents a trigonal pyramidal geometry. Rotational parameters are determined at the equilibrium and in selected vibrational states. For the ground state, the rotational constants were calculated to be A0 = 7031.7237 MHz, B0 = 6920.1221 MHz, and C0 = 4223.3389 MHz, at few megahertz from the previous experimental measurements. Ab initio calculations allow us to assert that DMSO rotational constants are strongly dependent on anharmonic effects. Asymmetry increases with the vibrational energy. Harmonic frequencies, torsional parameters, and a two-dimensional potential energy surface (2D-PES) focused to describe the internal rotation of the two methyl groups are determined at the CCSD(T)-F12 level of theory. For the medium and small amplitude motions, anharmonic effects are estimated with MP2 theory getting an excellent agreement with experimental data for the ν11 and ν23 fundamentals. Torsional energies and transitions are computed variationally form the 2D-PES that denotes strong interactions between both internal tops. The vibrationally corrected V3 torsional barrier is evaluated to be 965.32 cm(-1). The torsional splitting of the ground vibrational state has been estimated to be lower than 0.01 cm(-1). Although the ν13 torsional fundamental is found at 229.837 cm(-1) in good agreement with previous assessment, there is not accord for the low intense transition ν24. A new assignment predicting ν24 to lie between 190 and 195 cm(-1) is proposed.

Theoretical characterization of dimethyl carbonate at low temperatures.

Highly correlated ab initio methods (CCSD(T) and RCCSD(T)-F12) are employed for the spectroscopic characterization of the gas phase of dimethyl carbonate (DMC) at low temperatures. DMC, a relevant molecule for atmospheric and astrochemical studies, shows only two conformers, cis-cis and trans-cis, respectively, of C2v and Cs symmetries. cis-cis-DMC represents the most stable form. Using RCCSD(T)-F12 theory, the two sets of equilibrium rotational constants have been computed to be Ae = 10 493.15 MHz, Be = 2399.22 MHz, and Ce = 2001.78 MHz (cis-cis) and to be Ae = 6585.16 MHz, Be = 3009.04 MHz, and Ce = 2120.36 MHz (trans-cis). Centrifugal distortions constants and anharmonic frequencies for all of the vibrational modes are provided. Fermi displacements are predicted. The minimum energy pathway for the cis-cis → trans-cis interconversion process is restricted by a barrier of ∼3500 cm(-1). DMC displays internal rotation of two methyl groups. If the nonrigidity is considered, the molecule can be classified in the G36 (cis-cis) and the G18 (trans-cis) symmetry groups. For cis-cis-DMC, both internal tops are equivalent, and the torsional motions are restricted by V3 potential energy barriers of 384.7 cm(-1). trans-cis-DMC shows two different V3 barriers of 631.53 and 382.6 cm(-1). The far-infrared spectra linked to the torsional motion of both conformers are analyzed independently using a variational procedure and a two-dimensional flexible model. In cis-cis-DMC, the ground vibrational state splits into nine components: one nondegenerate, 0.000 cm(-1) (A1), four quadruply degenerate, 0.012 cm(-1) (G), and four doubly degenerate 0.024 cm(-1) (E1 and E3). The methyl torsional fundamentals are obtained to lie at 140.274 cm(-1) (ν15) and 132.564 cm(-1) (ν30).

Theoretical spectroscopic characterization at low temperatures of methyl hydroperoxide and three S-analogs.

The low temperature spectra of the detectable species methyl hydroperoxide (CH3OOH) and three sulfur analogs, the two isomers of methanesulfenic acid (CH3SOH and CH3OSH) and the methyl hydrogen disulfide (CH3SSH), are predicted from highly correlated ab initio methods (CCSD(T) and CCSD(T)-F12). Rotational parameters, anharmonic frequencies, torsional energy barriers, torsional energy levels, and their splittings are provided. Our computed parameters should help for the characterization and the identification of these organic compounds in laboratory and in the interstellar medium.

Theoretical spectroscopic characterization at low temperatures of S-methyl thioformate and O-methyl thioformate.

Highly correlated ab initio methods are employed to determine spectroscopic properties at low temperatures of two S-analogs of methyl formate: S-methyl thioformate CH3-S-CHO (MSCHO) and O-methyl thioformate CH3-O-CHS (MOCHS). Both species are detectable and they are expected to play an important role in Astrochemistry. Molecular properties are compared with those of the O-analog, methyl formate. Both isomers present two conformers cis and trans. cis-CH3-S-CHO represents the most stable structure lying 4372.2 cm(-1) below cis-CH3-O-CHS. The energy difference between the cis and trans forms is drastically lower for MSCHO (1134 cm(-1)) than for MOCHS (1963.6 cm(-1)). Harmonic and anharmonic fundamentals and the corresponding intensities, as well as the rotational constants for the ground vibrational and first excited torsional states and the centrifugal distortions constants, are provided. Low torsional energy levels have been obtained by solving variationally a two dimensional Hamiltonian expressed in terms of the two torsional degrees of freedom. The corresponding 2D potential energy surfaces have been computed at the CCSD(T)/aug-cc-pVTZ level of theory. The methyl torsional barriers V3(cis) are determined to be 139.7 cm(-1) (CH3-S-CHO) and 670.4 cm(-1) (CH3-O-CHS). The A/E splitting of ground torsional state has been estimated to be 0.438 cm(-1) for CH3-S-CHO and negligible for CH3-O-CHS.

On the use of explicitly correlated treatment methods for the generation of accurate polyatomic -He/H2 interaction potential energy surfaces: The case of C3-He complex and generalization.

Through the study of the C3(X1Σg (+)) (1)Σg (+)) + He((1)S) astrophysical relevant system using standard (CCSD(T)) and explicitly correlated (CCSD(T)-F12) coupled cluster approaches, we show that the CCSD(T)-F12/aug-cc-pVTZ level represents a good compromise between accuracy and low computational cost for the generation of multi-dimensional potential energy surfaces (PESs) over both intra- and inter-monomer degrees of freedom. Indeed, the CCSD(T)-F12/aug-cc-pVTZ 2D-PES for linear C3 and the CCSD(T)-F12/aug-cc-pVTZ 4D-PES for bent C3 configurations gently approach those mapped at the CCSD(T)/aug-cc-pVXZ (X = T,Q) + bond functions level, whereas a strong reduction of computational effort is observed. After exact dynamical computations, the pattern of the rovibrational levels of the intermediate C3-He complex and the rotational and rovibrational (de-) excitation of C3 by He derived using both sets of PESs agree quite well. Since C3 shows a floppy character, the interaction PES is defined in four dimensions to obtain realistic collisional parameters. The C-C-C bending mode, which fundamental lies at 63 cm(-1) and can be excited at very low temperatures is explicitly considered as independent coordinate. Our work suggests hence that CCSD(T)-F12/aug-cc-pVTZ methodology is the key method for the generation of accurate polyatomic - He/H2 multi-dimensional PESs.

Theoretical spectroscopic characterization at low temperatures of detectable sulfur-organic compounds: ethyl mercaptan and dimethyl sulfide.

Highly correlated ab initio methods are used for the spectroscopic characterization of ethyl mercaptan (CH3CH2 (32)SH, ETSH) and dimethyl sulfide (CH3 (32)SCH3, DMS), considering them on the vibrational ground and excited torsional states. Since both molecules show non-rigid properties, torsional energy barriers and splittings are provided. Equilibrium geometries and the corresponding rotational constants are calculated by means of a composite scheme based on CCSD(T) calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The ground and excited states rotational constants are then determined using vibrational corrections obtained from CCSD/cc-pVTZ force-field calculations, which are also employed to determine anharmonic frequencies for all vibrational modes. CCSD(T) and CCSD force fields are employed to predict quartic and sextic centrifugal-distortion constants, respectively. Equilibrium rotational constants are also calculated using CCSD(T)-F12. The full-dimensional anharmonic analysis does not predict displacements of the lowest torsional excited states due to Fermi resonances with the remaining vibrational modes. Thus, very accurate torsional transitions are calculated by solving variationally two-dimensional Hamiltonians depending on the CH3 and SH torsional coordinates of ethyl mercaptan or on the two methyl groups torsions of dimethyl-sulfide. For this purpose, vibrationally corrected potential energy surfaces are computed at the CCSD(T)/aug-cc-pVTZ level of theory. For ethyl mercaptan, calculations show large differences between the gauche (g) and trans (t) conformer spectral features. Interactions between rotating groups are responsible for the displacements of the g-bands with respect to the t-bands that cannot therefore be described with one-dimensional models. For DMS, the CCSD(T) potential energy surface has been semi-empirically adjusted to reproduce experimental data. New assignments are suggested for the methyl torsion bands of ETSH and a reassignment is proposed for the infrared bands of DMS (0 3 → 0 4 and 1 0 → 1 1). Our accurate spectroscopic data should be useful for the analysis of the microwave and far infrared spectra of ETSH and DMS recorded, at low temperatures, either in laboratory or in the interstellar medium.

WT1 isoform expression pattern in acute myeloid leukemia.

WT1 plays a dual role in leukemia development, probably due to an imbalance in the expression of the 4 main WT1 isoforms. We quantify their expression and evaluate them in a series of AML patients. Our data showed a predominant expression of isoform D in AML, although in a lower quantity than in normal CD34+ cells. We found a positive correlation between the total WT1 expression and A, B and C isoforms. The overexpression of WT1 in AML might be due to a relative increase in A, B and C isoforms, together with a relative decrease in isoform D expression.

Theoretical characterization of C7, C7-, and C7+.

We present a theoretical investigation of neutral and ionic C7 molecules. Since carbon chains present isomerism and the number of possible structures increases fast with the number of carbon atoms, a B3LYP∕aug-cc-pVTZ search of stationary points has been achieved. For C7, we found twelve minimal structures. Among these forms, eleven C7 isomers are located into the lowest singlet hyper potential energy surface. The most stable form of C7 is linear and possesses a (1)Σg(+) symmetry species. For C7(-), we characterized fifteen stable forms, where twelve are of doublet spin-multiplicity. The global minimum of C7(-) is a (2)Πg doubly degenerate Renner-Teller structure. For C7(+) cation, we found eleven doublet and three quartet isomers with a 7-atom cycle, C7(+) (X(2)A1) ground state. For the most stable forms, explicitly correlated (R)CCSD(T)-F12 calculations have been performed for the determination of equilibrium geometries and for the spectroscopic characterization of C7, C7(-), and C7(+), providing accurate rotational constants and harmonic frequencies. Vertical excitation energies to the lowest electronic states have been computed at the CASSCF∕MRCI∕aug-cc-pVTZ level. Thirty five electronic states of C7, suitable of being involved in reactive processes, lie below 7 eV. Fourteen metastable electronic states of C7(-) have been found below 3.5 eV. For linear-C7, we compute the electron affinity and the ionization energy to be 3.38 eV and 10.42 eV, respectively.

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Highly correlated ab initio study of the low frequency modes of propane and various monosubstituted isotopologues containing D and 13C.

With the purpose of providing some clues that could encourage the spectral recordings of propane and various monodeuterated and (13)C isotopologues and also to explore their far infrared spectra at low temperatures, the energy levels corresponding to their three lowest frequency modes are determined variationally using a flexible model in three dimensions. Five vibrationally corrected potential energy surfaces are computed using CCSD(T) ab initio calculations. In spite of the quality of these highly correlated potentials in molecules with similar structures, it was proven that an empirical adjustment of the surfaces would enclose accurately the experimental and theoretical frequency residuals and therefore it is also used in the present work. Interacting terms, energy levels and tunneling splittings are provided for CH3CH2CH3, CH3(13)CH2CH3, (13)CH3CH2CH3, CH2DCH2CH3 and CH3CHDCH3. Infrared and Raman transitions of CH3CH2CH3 are assigned. Correlation between symmetry species of the five isotopologue symmetry groups (G36, G36, G18, G6 and G'18, respectively) is established for the classification of the levels and torsional splittings. The rotational constants are determined with CCSD(T)/CBS (A0 = 29263.46 MHz, B0 = 8454.10 MHz and C0 = 7466.64 MHz) using a non-relativistic procedure. Fundamental anharmonic frequencies corresponding to the high and medium amplitude modes are computed for all the isotopologues. The adjusted parameters are accurate enough to be employed in further spectral analysis.

Highly correlated ab initio study of the far infrared spectra of methyl acetate.

Highly correlated ab initio calculations (CCSD(T)) are used to compute gas phase spectroscopic parameters of three isotopologues of the methyl acetate (CH(3)COOCH(3), CD(3)COOCH(3), and CH(3)COOCD(3)), searching to help experimental assignments and astrophysical detections. The molecule shows two conformers cis and trans separated by a barrier of 4457 cm(-1). The potential energy surface presents 18 minima that intertransform through three internal rotation motions. To analyze the far infrared spectrum at low temperatures, a three-dimensional Hamiltonian is solved variationally. The two methyl torsion barriers are calculated to be 99.2 cm(-1) (C-CH(3)) and 413.1 cm(-1) (O-CH(3)), for the cis-conformer. The three fundamental torsional band centers of CH(3)COOCH(3) are predicted to lie at 63.7 cm(-1) (C-CH(3)), 136.1 cm(-1) (O-CH(3)), and 175.8 cm(-1) (C-O torsion) providing torsional state separations. For the 27 vibrational modes, anharmonic fundamentals and rovibrational parameters are provided. Computed parameters are compared with those fitted using experimental data.

Analysis of SNP rs16754 of WT1 gene in a series of de novo acute myeloid leukemia patients.

The single nucleotide polymorphism (SNP) rs16754 of the WT1 gene has been previously described as a possible prognostic marker in normal karyotype acute myeloid leukemia (AML) patients. Nevertheless, the findings in this field are not always reproducible in different series. One hundred and seventy-five adult de novo AML patients were screened with two different methods for the detection of SNP rs16754: high-resolution melting (HRM) and FRET hybridization probes. Direct sequencing was used to validate both techniques. The SNP was detected in 52 out of 175 patients (30 %), both by HRM and hybridization probes. Direct sequencing confirmed that every positive sample in the screening methods had a variation in the DNA sequence. Patients with the wild-type genotype (WT1(AA)) for the SNP rs16754 were significantly younger than those with the heterozygous WT1(AG) genotype. No other difference was observed for baseline characteristic or outcome between patients with or without the SNP. Both techniques are equally reliable and reproducible as screening methods for the detection of the SNP rs16754, allowing for the selection of those samples that will need to be sequenced. We were unable to confirm the suggested favorable outcome of SNP rs16754 in de novo AML.

Rapid screening of ASXL1, IDH1, IDH2, and c-CBL mutations in de novo acute myeloid leukemia by high-resolution melting.

Recently, many novel molecular abnormalities were found to be distinctly associated with acute myeloid leukemia (AML). However, their clinical relevance and prognostic implications are not well established. We developed a new combination of high-resolution melting assays on a LightCycler 480 and direct sequencing to detect somatic mutations of ASXL1 (exon 12), IDH1 (exon 4), IDH2 (exon 4), and c-CBL (exons 8 and 9) genes to know their incidence and prognostic effect in a cohort of 175 patients with de novo AML: 16 patients (9%) carried ASXL1 mutations, 16 patients had IDH variations (3% with IDH1(R132) and 6% with IDH2(R140)), and none had c-CBL mutations. Patients with ASXL1 mutations did not harbor IDH1, [corrected] or CEBPA mutations, and a combination of ASXL1 and IDH2 mutations was found only in one patient. In addition, we did not find IDH1 and FLT3 or CEBPA mutations concurrently or IDH2 with CEBPA. IDH1 and IDH2 mutations were mutually exclusive. Alternatively, NPM1 mutations were concurrently found with ASXL1, IDH1, or IDH2 with a variable incidence. Mutations were not significantly correlated with any of the clinical and biological features studied. High-resolution melting is a reliable, rapid, and efficient screening technique for mutation detection in AML. The incidence for the studied genes was in the range of those previously reported. We were unable to find an effect on the outcome.