Conformations of dimethoxymethane: matrix isolation infrared and ab initio studies

Conformations of dimethoxymethane (DMM) were studied using matrix isolation infrared spectroscopy. DMM was trapped in an argon matrix using an effusive source at 298, 388 and 430 K. Experiments were also done using a supersonic jet source to look for conformational cooling in the expansion process. As a result of these experiments, spectrally resolved infrared features of the ground and first higher energy conformer of DMM have been recorded, for the first time. The experimental studies were supported by ab initio computations performed at HF and B3LYP levels, using a 6-31++G** basis set. Computationally, four minima were identified corresponding to conformers with GG, TG, G+G- and TT structures. The computed frequencies at the B3LYP level were found to compare well with the experimental matrix isolation frequencies, leading to a definitive assignment of the infrared features of DMM, for the GG and TG conformers. At the B3LYP/6-31++G** level, the energy difference between the GG and TG conformers was computed to be 2.30 kcal mol(-1). The barrier for conformation interconversion, TG-->GG level was calculated to be 0.95 kcal mol(-1). This value is consistent with the experimental observation that the spectral features due to the TG conformer disappeared in the matrix on annealing.     

Matrix isolation infrared and ab initio study of the conformations of 2,2-dimethoxypropane

Conformations of 2,2-dimethoxypropane (DMP) were studied using matrix isolation infrared spectroscopy. An effusive source maintained at different temperatures (298, 388 and 430 K) was used to deposit DMP in a nitrogen matrix. As a result of these experiments, spectrally resolved infrared features of the ground and first higher energy conformer of DMP have been recorded, for the first time. The experimental studies were supported by ab initio computations performed at B3LYP/6-31++G** level. Computationally, four minima were identified corresponding to conformers with G+/-G-/+, TG+/-, G+/-G+/- and TT structures. The computed frequencies at the B3LYP level were found to compare well with the experimental matrix isolation frequencies, leading to a definitive assignment of the infrared features of DMP, for the G+/-G-/+ and TG+/- conformers. At the B3LYP/6-31++G** level, the energy difference between the G+/-G-/+ and TG+/- conformers was computed to be 3.25 kcal x mol(-1). The barrier for conformation interconversion, TG+/--->G+/-G-/+, was calculated to be 1.29 kcal x mol(-1). The magnitude of this barrier is consistent with the experimental observation that the spectral features due to the TG+/- decreased considerably in intensity when the matrix was annealed.     

Conformations of trimethyl phosphite: a matrix isolation infrared and ab initio study

The conformations of trimethyl phosphite (TMPhite) were studied using matrix isolation infrared spectroscopy. TMPhite was trapped in a nitrogen matrix using an effusive source maintained at two different temperatures (298 and 410 K) and a supersonic jet source. The experimental studies were supported by ab initio computations performed at the B3LYP/6-31++G** level. Computations identified four minima for TMPhite, corresponding to conformers with C(1)(TG(±)G(±)), C(s)(TG(+)G(-)), C(1)(G(±)TT), and C(3)(G(±)G(±)G(±)) structures, given in order of increasing energy. Computations of the transition state structures connecting the C(s)(TG(+)G(-)) and C(1)(G(±)TT) conformers to the global minimum C(1)(TG(±)G(±)) structure were also carried out. The barriers for the interconversion of C(s)(TG(+)G(-)) and C(1)(G(±)TT) to the ground state C(1)(TG(±)G(±)) conformer were 0.2 and 0.6 kcal/mol, respectively. Comparison of conformational preferences of TMPhite with the related carbon compound, trimethoxymethane, and the organic phosphate, trimethyl phosphate, was also made using natural bond orbital analysis.     

Conformations of dimethoxydimethylsilane: matrix isolation infrared and ab initio studies

Conformations of dimethoxydimethylsilane (DMDMS) were studied using matrix isolation infrared spectroscopy, by trapping the silane in argon and nitrogen matrixes. The matrix was deposited using both an effusive and a supersonic jet source. The effusive source was maintained at two different temperatures, viz. 298 and 433 K, during deposition to alter the conformational population of the silane. The experimental results were supported by computations performed at both the HF and B3LYP levels, using 6-31++G** basis set. Vibrational frequency calculations were carried out to assign the experimental features and also to ensure that the computed structures did indeed correspond to minima. A conformer with a G+/-G-/+ structure was found to be the ground state, while G+/-T and G+/-G+/- structures were the next higher energy conformers with energies of 1.32 and 1.48 kcal/mol, respectively. Natural bond orbital analysis was carried out at both HF/6-31++G** and B3LYP/6-31++G** level which indicated that the charge-transfer hyperconjugative interactions largely determine the conformational preferences in this molecule. This interaction appears to be smaller in DMDMS than in the corresponding carbon analogue, dimethoxypropane (DMP).     

Structure of the boronic acid dimer and the relative stabilities of its conformers

Despite the widespread use of boronic acids in materials science and as pharmaceutical agents, many aspects of their structure and reactivity are not well understood. In this research the boronic acid dimer, [HB(OH)(2)](2), was studied by second-order M?ller-Plesset (MP2) perturbation theory and coupled cluster methodology with single and double excitations (CCSD). Pople split-valence 6-31+G*, 6-311G**, and 6-311++G** and Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the calculations. A doubly hydrogen-bonded conformer (1) of the dimer was consistently found to be lowest in energy; the structure of 1 was planar (C(2h)) at most computational levels employed but was significantly nonplanar (C(2)) at the MP2/6-311++G** and CCSD/6-311++G** levels, the result of an intrinsic problem with Pople-type sp-diffuse basis functions on heavy atoms. The dimerization energy, enthalpy, and free energy for the formation of (1) from the exo-endo conformer of the monomer were -10.8, -9.2, and +1.2 kcal/mol, respectively, at the MP2/aug-cc-pVTZ level. Several other hydrogen-bonded conformers of the dimer were local minima on the potential energy surface (PES) and ranged from 2 to 5 kcal/mol higher in energy than 1. Nine doubly OH-bridged conformers, in which the boron atoms were tetracoordinated, were also local minima on the PES, but they were all greater than 13 kcal/mol higher in energy than 1; doubly H-bridged structures proved to be transition states. MP2 and CCSD results were compared to those from the BLYP, B3LYP, OLYP, O3LYP, PBE1PBE, and TPSS functionals with the 6-311++G** and aug-cc-pVTZ basis sets; the PBE1PBE functional performed best relative to the MP2 and CCSD results. Self-consistent reaction field (SCRF) calculations predict that boronic acid dimerization is less favorable in solution than in vacuo.     

The C7-C10 cycloalkanes revisited

The conformers of cycloheptane through cyclodecane have been examined at the B3LYP/6-311+G* and MP2/6-311+G* theoretical levels, with some additional calculations at the CCD/6-311+G* and CCSD(T)/6-311++G** levels. With cyclooctane, B3LYP predicts that the boat-chair and crown conformers have similar energies, whereas MP2 and CCSD(T) predict that the crown conformer is 2 kcal/mol higher in energy. The latter is in agreement with the electron diffraction data. With cyclononane, B3LYP predicts that two of the higher-energy conformers found in molecular mechanics calculations should convert to one of the lower-energy conformers. However, MP2/6-311+G* optimizations find them to be true minima on the potential energy surface. B3LYP systematically predicts larger C-C-C bond angles for these compounds than either MP2 or CCD. The results of molecular mechanics MM4 calculations are generally in good agreement with those obtained using MP2.     

Density functional theory studies of conformational stabilities and rotational barriers of 2- and 3-thiophenecarboxaldehydes

The molecular structures, conformational stabilities, and infrared vibrational wavenumbers of 2-thiophenecarboxaldehyde and 3-thiophenecarboxaldehyde are computed using Becke-3–Lee–Yang–Parr (B3LYP) with the 6-311++G** basis set. From the computations, cis-2-thiophenecarboxaldehyde is found to be more stable than the transfer conformer with an energy difference of 1.22 kcal/mol, while trans-3-thiophenecarboxaldehyde is found to be more stable than the cis conformer by 0.89 kcal/mol. The computed dipole moments, structural parameters, relative stabilities of the conformers and infrared vibrational wavenumbers of the two molecules coherently support the experimental data in the literature. The normal vibrational wavenumbers are characterized in terms of the potential energy distribution using the VEDA4 program. The effect of solvents on the conformational stability of the molecules in nine different solvents is investigated using the polarizable continuum model.     

Potential energy distributions and potential scans for the internal rotation of two rotors in 3,3-dichloro and 3,3,3-trichloropropanals.

The conformational behavior and structural stability of 3,3-dichloropropanal and 3,3,3-trichloropropanal were investigated by ab initio calculations. The 6-311 + + G** basis set was employed to include polarization and diffuse functions in the calculations at B3LYP level. From the calculation, the trans conformer of 3,3,3-trichloropropanal was predicted to be the predominant conformer with about 2 kcal mol(-1) of energy lower than the cis form. Additionally, 3,3 dichloro-propanal was predicted to exist as a mixture of three stable conformers. The potential function scans were calculated for the two molecules from which the rotational barriers could be estimated. The vibrational frequencies were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations for the conformers of the two molecules. Vibrational Raman and infrared spectra of the mixture of the stable conformers were computed at 300 K.     

Substituent effects on structural stability of formyl ketene and analysis of vibrational spectra of formyl haloketenes and formyl methylketene.

The conformational behavior and the structural stability of formyl fluoroketene, formyl chloroketene and formyl methylketene were investigated by utilizing quantum mechanical DFT calculations at B3LYP/6-31I + + G** and ab initio calculations at MP2/6-311 + + G** levels. The three molecules were predicted to have a planar s-cis<-->s-trans conformational equilibrium. From the calculations, the direction of the conformational equilibrium was found to be dependent on the nature of the substituting group. In formyl haloketenes, the cis conformation, where the C=O group eclipses the ketenic group, was expected to be of lower energy than the trans conformer. In the case of formyl methylketene the conformational stability was reversed and the trans form (the aldehydic hydrogen eclipsing the ketenic group) was calculated to be about 2 kcal mol(-1) lower in energy than the cis form. The calculated cis-trans energy barrier was found to be in the order: fluoride (15.3 kcal mol(-1)) > chloride (13.1 kcal mol(-1)) > methyl (11.7 kcal mol(-1). Full optimization was performed at the ground and the transition states of the molecules. The vibrational frequencies for the stable conformers of the three ketenic systems were computed at the DFT-B3LYP level, and the zero-point corrections were included into the calculated rotational barriers. Complete vibrational assignments were made on the basis of both normal coordinate calculations and comparison with experimental results of similar molecules.     

A computational study of conformational interconversions in 1,4-dithiacyclohexane (1,4-dithiane)

Ab initio molecular orbital theory with the 6-31G(d), 6-31G(d,p), 6-31+G(d), 6-31+G(d,p), 6-31+G(2d,p), 6-311G(d), 6-311G(d,p), and 6-311+G(2d,p) basis sets and density functional theory (BLYP, B3LYP, B3P86, B3PW91) have been used to locate transition states involved in the conformational interconversions of 1,4-dithiacyclohexane (1,4-dithiane) and to calculate the geometry optimized structures, relative energies, enthalpies, entropies, and free energies of the chair and twist conformers. In the chair and 1,4-twist conformers the C-Hax and C-Heq bond lengths are equal at each carbon, which suggest an absence of stereoelectronic hyperconjugative interactions involving carbon-hydrogen bonds. The 1,4-boat transition state structure was 9.53 to 10.5 kcal/mol higher in energy than the chair conformer and 4.75 to 5.82 kcal/mol higher in energy than the 1,4-twist conformer. Intrinsic reaction coordinate (IRC) calculations showed that the 1,4-boat transition state structure was the energy maximum in the interconversion of the enantiomers of the 1,4-twist conformer. The energy difference between the chair conformer and the 1,4-twist conformer was 4.85 kcal/mol and the chair-1,4-twist free energy difference (deltaG degrees (c-t)) was 4.93 kcal/mol at 298.15 K. Intrinsic reaction coordinate (IRC) calculations connected the transition state between the chair conformer and the 1,4-twist conformer. This transition state is 11.7 kcal/mol higher in energy than the chair conformer. The effects of basis sets on the 1,4-dithiane calculations and the relative energies of saturated and unsaturated six-membered dithianes and dioxanes are also discussed.     

Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations

Ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2‐methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets. The 6‐31G* and 6‐311++G** basis sets make up the B3LYP/6‐31G* and B3LYP/6‐311++G** procedures. Internal coordinates were fully relaxed, and structures were gradient optimized at both levels of theory. Ten conformations were studied at the B3LYP/6‐31G* level, and five of these were continued with full gradient optimization at the B3LYP/6‐311++G** level of theory. The details of the ab initio optimized geometries are presented here, with particular attention given to the positions of the atoms around the anomeric center and the effect of the particular anomer and hydrogen bonding pattern on the maltose ring structures and relative conformational energies. The size and complexity of the hydrogen‐bonding network prevented a rigorous search of conformational space by ab initio calculations. However, using empirical force fields, low‐energy conformers of maltose were found that were subsequently gradient optimized at the two ab initio levels of theory. Three classes of conformations were studied, as defined by the clockwise or counterclockwise direction of the hydroxyl groups, or a flipped conformer in which the ψ‐dihedral is rotated by ∼180°. Different combinations of ω side‐chain rotations gave energy differences of more than 6 kcal/mol above the lowest energy structure found. The lowest energy structures bear remarkably close resemblance to the neutron and X‐ray diffraction crystal structures. © 2000 John Wiley & Sons, Inc. * J Comput Chem 21: 1204–1219, 2000     

Conformers and intramolecular hydrogen bonding of the oxalic acid monomer and its anions

Density functional theory, B3LYP/6‐31G** and B3LYP/6‐311+G(2d,p), and ab initio MP2/6‐31G** calculations have been carried out to investigate the conformers, transition states, and energy barriers of the conformational processes of oxalic acid and its anions. QCISD/6‐31G** geometrical optimization is also performed in the stable forms. Its calculated energy differences between the two most stable conformers are very near to the related observed value at 7.0 kJ/mol. It is found that the structures and relative energies of oxalic acid conformers predicted by these methods show similar results, and that the conformer L1 (C_2h) with the double‐interfunctional‐groups hydrogen bonds is the most stable conformer. The magnitude of hydrogen bond energies depends on the energy differences of various optimized structures. The hydrogen bond energies will be about 32 kJ/mol for interfunctional groups, 17 kJ/mol for weak interfunctional groups, 24 kJ/mol for intra‐COOH in (COOH)₂, and 60 kJ/mol for interfunctional groups in (COOH)COO⁻¹ ion if calculated using the B3LYP/6‐311+G(2d,p) method. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 541–551, 2000     

Conformational energies for 2-substituted butanes

The conformational free energies for some 2-substituted butanes where X = F, Cl, CN, and CCH were calculated using G3-B3, CBS-QB3, and CCSD(T)/6-311++G(2d,p) as well as other theoretical levels. The above methods gave consistent results with free energies relative to the trans conformers as follows: X = CCH, g+ = 0.77 +/- 0.05 kcal/mol. g- = 0.88 +/- 0.05 kcal/mol; X = CN, g+ = 0.85 +/- 0.05 kcal/mol, g- = 0.75 +/- 0.05 kcal/mol; X = Cl, g+ = 0.70 +/- 0.05 kcal/ml, g- = 0.80 +/- 0.05 kcal/mol; and X = F, g+ = 0.53 +/- 0.05 kcal/mol, g- = 0.83 +/- 0.05 kcal/mol. The conformational free energies also were estimated using the observed liquid phase IR spectra and intensities calculated using B3LYP/6-311++G** and MP2/6-311++G**. The rotational free energy profiles for all of the compounds were estimated at the G3-B3 level.     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

Structures of protonated arginine dimer and bradykinin investigated by density functional theory: further support for stable gas-phase salt bridges

The gas-phase structures and energetics of both protonated arginine dimer and protonated bradykinin were investigated using a combination of molecular mechanics with conformational searching to identify candidate low-energy structures, and density functional theory for subsequent minimization and energy calculations. For protonated arginine dimer, a good correlation (R = 0.88) was obtained between the molecular mechanics and EDF1 6-31+G* energies, indicating that mechanics with MMFF is suitable for finding low-energy conformers. For this ion, the salt-bridge or ion-zwitterion form was found to be 5.7 and 7.2 kcal/mol more stable than the simple protonated or ion-molecule form at the EDF1 6-31++G** and B3LYP 6-311++G** levels. For bradykinin, the correlation between the molecular mechanics and DFT energies was poor (R = 0.28), indicating that many low-energy structures are likely passed over in the mechanics conformational searching. This result suggests that structures of this larger peptide ion obtained using mechanics calculations alone are not necessarily reliable. The lowest energy structure of the salt-bridge form of bradykinin is 10.6 kcal/mol lower in energy (EDF1) than the lowest energy simple protonated form at the 6-311G* level. Similarly, the average energy of all salt-bridge structures investigated is 13.6 kcal/mol lower than the average of all the protonated forms investigated. To the extent that a sufficient number of structures are investigated, these results provide some additional support for the salt-bridge form of bradykinin in the gas phase.     

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.     

A new scheme for determining the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of glycine and alanine peptides

In this paper a new scheme was proposed to calculate the intramolecular hydrogen-bonding energies in peptides and was applied to calculate the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of the glycine and alanine peptides. The density-functional theory B3LYP6-31G(d) and B3LYP6-311G(d,p) methods and the second-order Moller-Plesset perturbation theory MP26-31G(d) method were used to calculate the optimal geometries and frequencies of glycine and alanine peptides and related structures. MP26-311++G(d,p), MP26-311++G(3df,2p), and MP2/aug-cc-pVTZ methods were then used to evaluate the single-point energies. It was found that the B3LYP6-31G(d), MP26-31G(d), and B3LYP6-311G(d,p) methods yield almost similar structural parameters for the conformers of the glycine and alanine dipeptides. MP2/aug-cc-pVTZ predicts that the intramolecular seven-membered ring N-H...O=C hydrogen-bonding strength has a value of 5.54 kcal/mol in glycine dipeptide and 5.73 and 5.19 kcal/mol in alanine dipeptides, while the steric repulsive interactions of the seven-membered ring conformers are 4.13 kcal/mol in glycine dipeptide and 6.62 and 3.71 kcal/mol in alanine dipeptides. It was also found that MP26-311++G(3df,2p) gives as accurate intramolecular N-H...O=C hydrogen-bonding energies and steric repulsive interactions as the much more costly MP2/aug-cc-pVTZ does.     

A quantum-chemical study of the LiH + LiH⋅− ⇄ LiH2− + Li⋅ reaction

Parts of the potential energy surface of the title process and related processes have been investigated at the SCF /6-31G **, SCF /6-31++G **, and MP 2/6-31++G ** levels. The investigated reaction is exothermic (?6.23 kcal/mol, MP 4/6-31++G **//MP 2/6–31++G** level, ZPE included): A linear intermediate radical anion, Li? H? Li? H??, is significantly stabilized with respect to LiH + LiH?? (?38.74 kcal/mol, the same level as above). The BSSE at MP 2/6–31++G **//MP 2/6–31++G ** amounts to 1.8 kcal/mol. The title process seems to be suitable for experimental study in molecular beams.