The extremely flat torsional potential energy surface of oxalyl chloride

The conformational behavior of oxalyl chloride has been investigated using ab initio Hartree-Fock (HF) and second-order Moller-Plesset (MP2) perturbation theories, and the coupled-cluster singles and doubles method appended with a perturbative inclusion of connected triple excitations [CCSD(T)]. Correlation consistent polarized valence quadruple-zeta (cc-pVQZ) and quintuple-zeta (cc-pV5Z) basis sets were used in this research. At the cc-pVQZ and cc-pV5Z HF levels, there is no stationary point corresponding to a stable gauche conformer. On the other hand, at the cc-pVQZ and cc-pV5Z MP2 levels and with the cc-pVQZ CCSD(T) method, the gauche conformer of oxalyl chloride was found at O[Double Bond]C-C[Double Bond]O dihedral angles of 81.9 degrees , 79.4 degrees , and 83.4 degrees , respectively. At the cc-pV5Z MP2 level, the energy barrier from trans to gauche was predicted to be 0.74 kcal mol(-1) and that from gauche to trans to be 0.09 kcal mol(-1). Thus, the potential-energy surface along the O[Double Bond]C-C[Double Bond]O torsional mode is exceedingly flat. The existence of the gauche conformation is mainly due to the minimization of steric repulsion.     

The effect of the torsional and stretching vibrations of C2H6 on the H + C2H6 --> H2 + C2H5 reaction

We present a three-dimensional quantum scattering model to treat reactions of the type H + C2H6 --> H2 + C2H5. The model allows the torsional and the stretching degrees of freedom to be treated explicitly. Zero-point energies of the remaining modes are taken into account in electronic structure calculations. An analytical potential-energy surface was developed from a minimal number of ab initio geometry evaluations using the CCSD(T,full)/cc-pVTZ//MP2(full)/cc-pVTZ level of theory. The reaction is endothermic by 1.5 kcal mol(-1) and exhibits a vibrationally adiabatic barrier of 12.0 kcal mol(-1). The results show that the torsional mode influences reactivity when coupled with the vibrational C-H stretching mode. We also found that ethyl radical products are formed internally excited in the torsional mode.     

Triplet excited state in platinum-acetylide oligomers: triplet localization and effects of conformation

An experimental and theoretical investigation was carried out on a series of platinum-acetylide oligomers of the general structure Ph-CC-[PtL2-CC-(1,4-Ph)-CC-]n-PtL2-CC-Ph (where n = 1, 2, 3, 4, 6; Ph = phenyl, 1,4-Ph = 1,4-phenylene; L = P(n-Bu)3, and the geometry at Pt = trans). The objective of this work is to understand the geometry and electronic structure of the ground and triplet excited states of Pt-acetylide oligomers. The experiments carried out include temperature-dependent absorption and photoluminescence spectroscopy (80-298 K range) and ambient temperature transient absorption spectroscopy. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out on several of the oligomers using the hybrid Becke's three-parameter functional with the B3LYP correlation functional and the SDD basis set. The combined experimental and theoretical results provide very clear evidence that the triplet excited state is localized on a chromophore consisting approximately of a single -[PtL2-CC-(1,4-Ph)-CC-PtL2]- repeat unit. DFT calculations indicate that in the ground state conformers that differ in the (rotational) orientation of the 1,4-phenylenes with respect to the plane defined by the PtL2(C)2 units (twisted = t and planar = p) are very close in energy (difference of <1 kcal.mol-1). By contrast, in the triplet excited state, the p conformer is 3 kcal.mol-1 lower in energy than the t conformer. The torsional geometry change in the triplet state is reflected in the low-temperature phosphorescence spectra of the short oligomers, where separate emission bands are seen from the t and p conformers.     

Matrix-isolation FT-IR spectra and theoretical study of dimethyl sulfate

The preferred conformations of dimethyl sulfate and their vibrational spectra were studied by matrix-isolation FT-IR spectroscopy and theoretical methods (DFT and MP2, with basis sets of different sizes, including the quadruple-zeta, aug-cc-pVQZ basis). Conformer GG (of C2 symmetry and exhibiting OSOC dihedral angles of 74.3 degrees ) was found to be the most stable conformer in both the gaseous phase and isolated in argon. Upon annealing of the matrix, the less stable observed conformer (GT; with C1 symmetry) quickly converts to the GG conformer, with the resulting species being embedded in a matrix-cage which corresponds to the most stable matrix-site for GG form. The highest energy TT conformer, which was assumed to be the most stable conformer in previous studies, is predicted by the calculations to have a relative energy of ca. 10 kJ mol-1 and was not observed in the spectra of the matrix-isolated compound.     

Potential energy scans and vibrational assignments of cyclopropanecarboxylic acid and cyclopropanecarboxamide

The structural stability and internal rotations in cyclopropanecarboxylic acid and cyclopropanecarboxamide were investigated by the DFT-B3LYP and the ab initio MP2 calculations using 6-311G** and 6-311+G** basis sets. The computations were extended to the MP4//MP2/6-311G** and CCSD(T)//MP2/6-311G** single-point calculations. From the calculations the molecules were predicted to exist predominantly in the cis (C=O group eclipses the cyclopropane ring) with a cis-trans barrier of about 4-6kcal/mol. The OCOH torsional barrier in the acid was estimated to be about 12-13kcal/mol while the corresponding OCNH torsional barrier in the amide was calculated to be about 20kcal/mol. The equilibrium constant k for the cis<-->trans interconversion in cyclopropanecarboxylic acid was calculated to be 0.1729 at 298.15K that corresponds to an equilibrium mixture of about 85% cis and 15% trans. The vibrational frequencies were computed at the DFT-B3LYP level. Normal coordinate calculations were carried out and potential energy distributions were calculated for the low energy cis conformer of the molecules. Complete vibrational assignments were made on the basis of normal coordinate calculations and comparison with experimental data of the molecules.     

Conformational dynamics of tetraisopropylmethane and of tetracyclopropylmethane

Tetraisopropylmethane (1) exists in solution as a mixture of two types of conformers (D2d and S4 time-averaged symmetry) in the ratio 93:7 at -110 degrees C, interconverting with a barrier of 9.7 kcal mol-1. Molecular mechanics calculations and the multiplicity of NMR signals at low temperature allow the assignment of these conformations. The only conformation populated in tetracyclopropylmethane (2) is the same type as the minor conformation (S4 time-averaged symmetry) populated in 1. 13C NMR spectra at about -180 degrees C show that degenerate versions of this conformation interconvert with a barrier of 4.5 kcal mol-1. Molecular mechanics calculations that characterize the six possible conformational types for these molecules, and the most important interconversion pathways, are reported. Calculated and experimental barriers match satisfactorily well.     

Conformational analysis of cis-2-halocyclohexanols; solvent effects by NMR and theoretical calculations

Conformational problems often involve very small energy differences, even low as 0.5 kcal mol(-1). This accuracy can be achieved by theoretical methods in the gas phase with the appropriate accounting of electron correlation. The solution behavior, on the other hand, comprises a much greater challenge. In this study, we conduct and analysis for cis-2-fluoro-, cis-2-chloro-, and cis-2-bromocyclohexanol using low temperature NMR experiments and theoretical calculations (DFT, perturbation theory, and classical molecular dynamics simulations). In the experimental part, the conformers' populations were measured at 193 K in CD(2)Cl(2), acetone-d(6), and methanol-d(4) solutions; the preferred conformer has the hydroxyl group in the equatorial and the halogen in the axial position (ea), and its population stays at about 60-70%, no matter the solvent or the halogen. Theoretical calculations, on the other hand, put the ae conformer at a lower energy in the gas phase (MP2/6-311++G(3df,2p)). Moreover, the theoretical calculations predict a markedly increase in the conformational energy on going from fluorine to bromine, which is not observed experimentally. The solvation models IEF-PCM and C-PCM were tested with two different approaches for defining the atomic radii used to build the molecular cavity, from which it was found that only with explicit consideration of hydrogens can the conformational preference be properly described. Molecular dynamic simulations in combination with ab initio calculations showed that the ea conformer is slightly favored by hydrogen bonding.     

A new enantiomerization mechanism for tripodal penta-coordinate Zn(II)(nta) complexes. Theoretical clarification of the observed 1H NMR spectrum

Based on DFT calculations (RB3LYP/LANL2DZp), the unexpected single-line 1H NMR spectrum of Zn(II)(nta), nta = 2,2',2'-nitrilotriacetate, can be ascribed to a non-dissociative enantiomerization process (deltadeltadelta<=>lambdalambdalambda) from C3viaC3v to C3 symmetry. The energy barrier is rather low and depends to a lesser extent on the nature of the co-ligand in [Zn(nta)X]2- (X: H-, CH3- NH2-, OCH3-, F-, Cl-, Br-, I-) and [Zn(nta)Y]- (Y: NCH, CO, N2, O(CH3)2), but more so on the overall charge of the complex. The energy barrier for enantiomerization of [Zn(nta)X]2- is between 5.7 and 6.7 kcal mol-1, and for [Zn(nta)Y]- between 2.2 and 3.1 kcal mol-1.     

A direct ab initio dynamics study of the water-assisted tautomerization of formamide

Direct ab initio dynamics calculations based on a canonical variational transition-state theory with several multidimensional semiclassical tunneling approximations were carried out to obtain rate constants for the water-assisted tautomerization of formamide. The accuracy of the density functionals, namely, B-LYP, B3-LYP, and BH&H-LYP, were examined. We found that the BH&H-LYP method yields the most accurate transition-state properties when comparing it to ab initio MP2 and QCISD results, whereas B-LYP and B3-LYP methods predict barrier heights too low. Reaction path information was calculated at both the MP2 and nonlocal hybrid BH&H-LYP levels using the 6–31G(d,p) basis set. At the BH&H-LYP level, we found that the zero-point energy motion lowers the barrier to tautomerization in the formamide-water complex by 3.6 kcal/mol. When tunneling is considered, the activation energy at the BH&H-LYP level at 300 K is 17.1 kcal/mol. This is 3.4 kcal/mol below the zero-point-corrected barrier and 7.0 kcal/mol below the classical barrier. Excellent agreement between BH&H-LYP and MP2 rate constants further supports the use of BH&H-LYP for rate calculations of large systems. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 861–874, 1997     

Structural studies of nonclassical cyclobutylmethyl cations by the ab initio method

Ab initio calculations at the MP2/cc-pVTZ level show that the cyclobutylmethyl cation is a nonclassical sigma-delocalized species, which is distinct from the global minimum C2-symmetric cyclopentyl cation (Schleyer, P. v. R.; Carneiro, J. W. de M.; Koch, W.; Raghavachari, K. J. Am. Chem. Soc. 1989, 111, 5475). Relatively lower level DFT calculations, on the other hand, show that the primary cyclobutylmethyl cation spontaneously collapses into the cyclopentyl cation (Prakash, G. K. S.; Reddy, V. P.; Rasul, G.; Casanova, J.; Olah, G. A. J. Am. Chem. Soc. 1998, 120, 13362). The secondary 1-cyclobutylethyl cation is also a nonclassical carbocation, as shown by calculations at the MP2/cc-pVTZ level. Two structures having energy minima are identified for the latter cation on the potential energy surface. The conformer in which the methyl group is in the exo orientation is a global minimum and is favored over the corresponding endo conformer by 1.2 kcal/mol at the MP2/cc-pVTZ//MP2/cc-pVTZ +ZPE level of calculations. The tertiary 1-cyclobutyl-1-methylethyl cation, at this level of calculations, also involves substantial nonclassical sigma-delocalization, showing that the nonclassical stabilization is more important for cyclobutylmethyl cations relative to the cyclopropylmethyl cations. The 13C NMR chemical shifts obtained from GIAO-CCSD(T)/tzp/dz calculations further substantiate the nonclassical structures for these carbocations.     

Conformational analysis of N-benzyl-N-o-tolyl-p-methylbenzene-sulfonamides from dynamic H NMR experiments and theoretical calculations

Theoretical studies of molecular conformations of four N-benzyl-N-o-tolyl-p-methylbenzenesulfonamides, by means of semiempirical PM3, ab initio (RHF and MP2) methods, and DFT approach, are presented and discussed in comparison with the experimental data. The free energy (ΔG^#) of rotation obtained by the dynamic shape analysis of the ¹H NMR spectra is ca. 16 kcal/mol for those systems for which the barrier has been probed experimentally. Failure to determine the barrier in the experimental spectra in the case of one system is attributed to the chiral conformation of the global minimum. The rotational profile was established at the PM3 level and verified at the DFT level of theory. The solvent effect, the 0th-order vibrational corrections, and the temperature dependence of the Boltzman distribution of conformers and kinetic equilibrium are discussed.     

Structure and conformations of N-(fluoroformyl)imidosulfurous dichloride,FC(O)N=SCl2

The IR (gas) and Raman (liquid) spectra of FC(O)NSCl(2) demonstrate the presence of a conformational mixture in both phases. According to a gas electron diffraction study, the main conformer (94(8)%) possesses a syn-syn structure (C(O)F group synperiplanar with respect to the SCl(2) bisector and the C=O bond synperiplanar to the N=S bond). Quantum chemical calculations (HF, B3LYP and MP2 with 6-31G basis set, and MP2/6-311(2df)) predict a syn-anti structure for the second conformer. Analysis of the IR (gas) spectrum results in a contribution of 5(1)% of the minor form, corresponding to a Gibbs free energy difference DeltaG degrees = G degrees (syn-anti) - G degrees (syn-syn) = 1.75(15) kcal/mol. This value is reproduced very well by quantum chemical calculations, which include electron correlation effects (DeltaG degrees = 1.28-1.56 kcal/mol). The HF approximation overestimates this energy difference (DeltaG degrees = 3.24 kcal/mol).     

Conformational stability, structural parameters and vibrational assignment from variable temperature infrared spectra of krypton solutions and ab initio calculations of ethylisothiocyanate

Variable temperature (-105 to -150 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylisothiocyanate, CH(3)CH(2)NCS, dissolved in liquid krypton have been recorded. Additionally the infrared spectra of the gas and solid have been re-investigated. These spectroscopic data indicate a single conformer in all physical states with a large number of molecules in the gas phase at ambient temperature in excited states of the CN torsional mode which has a very low barrier to conformational interchange. To aid in the analyses of the vibrational and rotational spectra, ab initio calculations have been carried out by the perturbation method to the second order (MP2) with valence and core electron correlation using a variety of basis sets up to 6-311+G(2df,2pd). With the smaller basis sets up to 6-311+G(d,p) and cc-PVDZ, the cis conformer is indicated as a transition state with all larger basis sets the cis conformer is the only stable form. The predicted energy difference from these calculations between the cis form and the higher energy trans conformer is about 125 cm(-1) which represents essentially the barrier to internal rotation of the NCS group (rotation around NC axis). Density functional theory calculation by the B3LYP method with the same basis sets predicts this barrier to be about 25 cm(-1). By utilizing the previously reported microwave rotational constants with the structural parameters predicted by the ab initio MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the cis form. The determined heavy atom parameters are: r(NC)=1.196(5), r(CS)=1.579(5), r(CN)=1.439(5), r(CC)=1.519(5)A for the distances and angles of angleCCN=112.1(5), angleCNC=146.2(5), angleNCS=174.0(5) degrees . The centrifugal distortion constants, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and compared to experimental quantities when available. These results are compared to the corresponding quantities of some similar molecules.     

Dimers of boroglycine and methylamine boronic acid: a computational comparison of the relative importance of dative versus hydrogen bonding

Boronic acids are widely used in materials science, pharmacology, and the synthesis of biologically active compounds. In this Article, geometrical structures and relative energies of dimers of boroglycine, H2N-CH2-B(OH)2, and its constitutional isomer H3C-NH-B(OH)2, were computed using second-order M?ller-Plesset perturbation theory and density functional theory; Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the MP2 calculations, and the Pople 6-311++G(d,p) basis set was employed for a majority of the DFT calculations. Effects of an aqueous environment were incorporated into the results using PCM and COSMO-RS methodology. The lowest-energy conformer of the H2N-CH2-B(OH)2 dimer was a six-membered ring structure (chair conformation; Ci symmetry) with two intermolecular B:N dative-bonds; it was 14.0 kcal/mol lower in energy at the MP2/aug-cc-pVDZ computational level than a conformer with the classic eight-centered ring structure (Ci symmetry) in which the boroglycine monomers are linked by a pair of H-O...H bonds. Compared to the results of MP2 calculations with correlation-consistent basis sets, DFT calculations using the PBE1PBE and TPSS functionals with the 6-311++G(d,p) basis set were significantly better at predicting relative conformational energies of the H2N-CH2-B(OH)2 and H3C-NH-B(OH)2 dimers than corresponding calculations using the BLYP, B3LYP, OLYP, and O3LYP functionals, particularly with respect to dative-bonded structures.     

Conformational studies by dynamic NMR. 78. Stereomutation of the helical enantiomers of trigonal carbon diaryl-substituted compounds: dimesitylketone, dimesitylthioketone, and dimesitylethylene.

The free energies of activation for the enantiomerization of the title compounds (Mes2C = X, Mes = 2,4,6-trimethylphenyl) were determined by dynamic NMR to be 4.6, 6.5, and 9.2 kcal mol-1 for X = O, S, and CH2, respectively. Single-crystal X-ray diffraction showed that the structure of dimesitylketone is that of a propeller (C2 symmetry) with the mesityl rings twisted by 50 degrees with respect to the plane of carbonyl. The same structure was predicted by molecular mechanics calculations, which also produced good agreement between computed and experimental barriers for a dynamic process where a disrotatory one-ring flip pathway reverses the helicity of the conformational enantiomers. Solid-state NMR spectra indicated that the enantiomerization barrier in the crystal must be much higher (at least 19 kcal mol-1) than that in solution. Contrary to the case of dimesitylketone, the calculated barrier of dimesitylethylene agrees better with the experimental value if the enantiomerization process is assumed to be a conrotatory two-ring flip pathway.     

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (i.e., parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster. To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments. For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O...H2O, H2O...Na+, and H2O...Cl- complexes have been explored. Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations. We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies. Our best estimate for the activation energy is 8.20 kcal/mol and for the reaction energy is -23.1 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory.     

Predictive chemical kinetics: Density functional and hartree–fock calculations on free-radial reaction transition states

Density functional theory (DFT ) using gradient-corrected «nonlocal» functionals is used to calculated the thermochemistry and barrier heights for several types of peroxyl radical isomerizations currently being studied by kineticists. The calculations are generally in good agreement with experimental data, where such data are available. An important exception is that the O—H bond strengths in hydroperoxides are all predicted to be too weak by about 7 kcal/mol. The calculated reaction barriers are a few kcal/mol lower than the experimental estimates, but comparable in accuracy to the much more computationally expensive second-order Møller–Plesset (MP 2) predictions. Various theoretical methods converge on a 42 ± 2 kcal/mole barrier for CH₃OO → H₂CO + OH. The DFT calculations can be used to predict reaction barriers in cases where no reliable experimental data are available. The effects of the choice of basis set and correlation functional are explored. Improvements needed to make these calculations most valuable to the chemical kineticist are discussed. © 1994 John Wiley & Sons, Inc.     

The isomerization of dinitrogen tetroxide: O2N-NO2 --> ONO-NO2

The N2O4 isomerization in gas phase has an energy barrier of 31 kcal mol-1 at 298 K. This energy barrier may be reduced due to the interaction of the N2O4 isomers with water or nitric acid clusters adsorbed on surfaces. The Gibbs free energy barrier for this reaction in water medium is estimated to be reduced to 21.1 kcal mol-1 by using the ab initio calculations and the polarizable continuum model (PCM). By using the transition state theory (TST), this model estimates that the N2O4 isomerization may be as fast as 2.0 x 10(-3) s-1 in aqueous phase at room temperature, which confirms the Finlayson-Pitts model for the heterogeneous hydrolysis of NO2 on surfaces. The activation energy of the N2O4 isomerization is about 21 kcal mol-1. The rate coefficient for this reaction is considerably fast, 1.2 x 10(-2) s-1, in aqueous phase at T = 373 K.     

Potential energy surface and quantum dynamics study of rovibrational states for HO(3) (X (2)A')

An analytic potential energy surface has been constructed by fitting to about 28 thousand energy points for the electronic ground-state (X (2)A') of HO(3). The energy points are calculated using a hybrid density functional HCTH and a large basis set aug-cc-pVTZ, i.e., a HCTH/aug-cc-pVTZ density functional theory (DFT) method. The DFT calculations show that the trans-HO(3) isomer is the global minimum with a potential well depth of 9.94 kcal mol(-1) with respect to the OH + O(2) asymptote. The equilibrium geometry of the cis-HO(3) conformer is located 1.08 kcal mol(-1) above that of the trans-HO(3) one with an isomerization barrier of 2.41 kcal mol(-1) from trans- to cis-HO(3). By using this surface, a rigorous quantum dynamics (QD) study has been carried out for computing the rovibrational energy levels of HO(3). The calculated results determine a dissociation energy of 6.15 kcal mol(-1), which is in excellent agreement with the experimental value of Lester et al. [J. Phys. Chem. A, 2007, 111, 4727.].