Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors

The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.     

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     

A conformational study of ethylene glycol

Ab initio calculations were performed for some different conformers of 1,2-ethanediol in order to reveal their relative energies. The equilibrium conformation is of gauche type with a comparatively weak intramolecular hydrogen bond. The energy of the all-trans conformer is 3 kcal/mol above the minimum.     

A microwave spectroscopic and quantum chemical study of 3-butyne-1-selenol (HSeCH2CH2C[triple bond]CH)

The microwave spectrum of 3-butyne-1-selenol has been studied by means of Stark-modulation microwave spectroscopy and quantum chemical calculations employing the B3LYP/aug-cc-pVTZ and MP2/6-311++G(3df,3pd) methods. Rotational transitions attributable to the H80SeCH2CH2C[triple bond]CH and H78SeCH2CH2C[triple bond]CH isotopologues of two conformers of this molecule were assigned. One of these conformers possesses an antiperiplanar arrangement for the atoms Se-C-C-C, while the other is synclinal and seems to be stabilized by the formation of a weak intramolecular hydrogen bond between the hydrogen atom of the selenol group and the pi electrons of the CC triple bond. The energy difference between these conformers was determined to be 0.2(5) kJ/mol by relative intensity measurements, and the hydrogen-bonded form was slightly lower in energy.     

Ab initio study of anomeric effect in 2,2-difluoroglycine

The optimized molecular structures of seven conformations of 2,2-difluoroglycine have been obtained from ab initio calculations. For conformers in which the lone pair of electrons on the nitrogen are antiperiplanar to one of the C–F bonds, that C–F bond is longer than the other C–F bond, which is synperiplanar to the lone pair of electrons. Conformers which have these features are the most stable conformers of those examined. This observation is explained in terms of an anomeric effect of the 1p(N)→σ^*(C–F). At the MP2/6-31G^* level of calculation, conformers IV and V are 21.5 and 18.7 kJ/mol, respectively, more stable than the least stable conformer, VI, which does not exhibit an anomeric effect. Conformer VII was found to be exceptionally stable, in addition to an anomeric effect, this conformer also exhibits features of a FH–O hydrogen bond.     

吡啶-BH~3相互作用复合物的理论研究

对吡啶-BH~3复合物分别用MP2/6-31+G^*和B3LYP/6-31+G^*进行理论计算以预测该复合物的构型及解离能，得到四种构型，在MP2优化构型基础上作CCSD/6-31+G^*单点能量计算以验证MP2与B3LYP结果的可靠性，然后用B3LYP作振动频率分析，计算了各构型的垂直电离势，最后用更大基组作单点能量计算和自然键轨道(NBO)分析。结果表明，N-B直接相连的构型最稳定，其解离能为141.50kJ/mol,MP2和B3LYP对N-H接近的构型结果相关较大，另外两种构型稳定性介于二者之间，解离能分别为15.18kJ/mol,14.06kJ/mol(MP2/6-31+G^*)。     

Conformers of gaseous proline

Accurate geometries, relative energies, rotational and quartic centrifugal distortion constants, dipole moments, harmonic vibrational frequencies, and infrared intensities were determined from ab initio electronic structure calculations for eighteen conformers of the neutral form of the amino acid L-proline. Only four conformers have notable population at low and moderate temperature. The second most stable conformer is only 2+/-2 kJ mol(-1) above the global minimum, while the third and fourth conformers are nearly degenerate and have an excess energy of 7+/-2 kJ mol(-1) relative to the global minimum. All four conformers have one hydrogen bond: N.HO in the lower energy pair of conformers, and NH.O in the higher energy pair of conformers. The conformer pairs differ only in their ring puckering. The relative energies of the conformers include corrections for valence electron correlation, extrapolated to the complete basis set limit, as well as core correlation and relativistic effects. Structural features of the pyrrolidine ring of proline are discussed by using the concept of pseudorotation. The accurate rotational and quartic centrifugal distortion constants as well as the vibrational frequencies and infrared intensities should aid identification and characterization of the conformers of L-proline by rotational and vibrational spectroscopy, respectively. Bonding features of L-proline, especially intramolecular hydrogen bonds, were investigated by the atoms-in-molecules (AIM) technique.     

An approach to estimate the energy and strength of the intramolecular hydrogen bond in different conformers of 4‐methylamino‐3‐penten‐2‐one

The molecular structure and intramolecular hydrogen bond energy of 32 conformers of 4‐methylamino‐3‐penten‐2‐one were investigated at MP2 and B3LYP levels of theory using the standard 6–31G** basis set and AIM analyses. Furthermore, calculations for all the possible conformations of 4‐methylamino‐3‐penten‐2‐one in water solution were also carried out at B3LYP/6–31G** level of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the ketoamine conformers of this compound are more stable than the other conformers (i.e., enolimine and ketoimine). This stability is mainly due to the formation of a strong N? H···O intramolecular hydrogen bond, which is assisted by π‐electrons resonance. Hydrogen bond energies for all conformers of 4‐methylamino‐3‐penten‐2‐one were obtained from the related rotamers method. The nature of intramolecular hydrogen bond existing within 4‐methylamino‐3‐penten‐2‐one has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. The results of these calculations support the results which obtained by related rotamers method. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Conformational study of monomeric 2,3-butanediols by matrix-isolation infrared spectroscopy and DFT calculations

The FT-IR spectra of two diastereomers of 2,3-butanediol, (R,S) and (S,S), isolated in low-temperature argon and xenon matrixes were studied, allowing the identification of two different conformers for each compound. These conformers were characterized by a +/-gauche arrangement around the O-C-C-O dihedral angle, thus enabling the establishment of a very weak intramolecular hydrogen bond of the O...H-O type. No other forms of these compounds were identified in matrixes, despite the fact that these four conformers had calculated relative energies from 0 to 5.1 kJ mol(-1) and were expected to be thermally populated from 50 to 6% in the gaseous phase of each compound. The nonobservation of additional conformers was explained in terms of low barriers to intramolecular rotation, resulting in the conformational relaxation of the compounds during deposition of the matrixes. The barriers to internal rotation of the OH groups were computed to be less than 4 kJ mol(-1) and are easily overcome in matrixes within the family of conformers with the same heavy atom backbone. The barriers for intramolecular rearrangement of the O-C-C-O dihedral angle in both diastereomers were calculated to range from 20 to 30 kJ mol(-1). Interconversions between the latter conformers were not observed in matrixes, even after annealing up to 65 K. Energy calculations, barriers, and calculated infrared spectra were carried out at the DFT(B3LYP)/6-311++G theory. Additional MP2/6-311++G calculations of energies and vibrational frequencies were performed on the most relevant conformers. Finally, independent estimations of the hydrogen-bond enthalpy in the studied molecules were also obtained based on theoretical structural data and from vibrational frequencies (using well-established empirical correlations). The obtained values for -DeltaH for both diastereomers of 2,3-butanediol amount to ca. 6-8 kJ mol(-1).     

Conformational behaviour, hydrogen bond competition and intramolecular dynamics in vanillin derivatives: acetovanillone and 6-hydroxy-3-methoxyacetophenone

The conformational landscape of the structural isomers acetovanillone (apocynin, AV) and 6-hydroxy-3-methoxyacetophenone (HMAP) has been investigated in a supersonic jet using Fourier transform microwave spectroscopy. Two conformers have been detected in the jet-cooled expansion for each molecule (s-cis and s-trans in AV; s-trans and a-trans for HMAP), differing in the relative orientation of the acetyl and methoxy groups. Both molecules are stabilized by O-H···O or O-H···O=C hydroxyl intramolecular hydrogen bonds, either constraining the local conformations of the methoxy group in AV, or that of the acetyl group in HMAP. Internal rotation splittings have been observed in both conformers of each molecule, originated by the acetyl group, that yield information on the influence of the intramolecular hydrogen bonds on the methyl torsion. The similar internal rotation barriers in both molecules (6.6 and 7.4 kJ mol(-1) in AV; 7.3 and 7.0 kJ mol(-1) in HMAP) suggest that the acetyl torsion is only slightly affected by intramolecular hydrogen bonding. The absence of torsional tunnellings due to the methoxy group indicates torsional barriers above 10.2 and 8.9 kJ mol(-1) for AV conformers, 10.1 and 10.4 kJ mol(-1) for HMAP. Conformational ratios and relative free energies have been estimated from relative intensity measurements of the spectral lines. Ab initio (MP2) and density functional calculations using the recent M05-2X empirical functional have been used to aid the experimental work in describing the structures, internal rotation barriers and isomerization potentials.     

Theoretical investigation of adenine–BX3 (X=F,Cl) complex

Geometries and binding energies are predicted at B3LYP/6-311+G* level for the adenine–BX₃ (X=F,Cl) systems and four conformers with no imaginary frequencies have been obtained for both adenine–BF₃ and adenine–BCl₃, respectively, and single energy calculations using much larger basis sets (6-311+G(2df,p)) and aug-cc-pVDZ were carried out as well. The most stable conformer is BF₃ or BCl₃ connected to N₃ of adenine and with the stabilization energy of 22.55 or 20.59 kcal/mol at B3LYP/6-311+G* level (BSSE corrected). The analyses for the combining interaction between BX₃ and adenine with natural bond orbital method (NBO) and the atom-in-molecules theory (AIM) have been performed. The results indicate that all the conformers were formed with σ–p type interactions between adenine and BX₃, in which pyridine-type nitrogen or nitrogen atom of amino group offers its lone pair electron to the empty p orbital of boron atom and the concomitances of charge transference from adenine to BX₃ were occurred. Frequency analysis suggested that the stretching vibration of BX₃ underwent a red shift in complexes. Adenine–BF₃ complex was more stable than adenine–BCl₃ although the distance of B–N is shorter in the later.     

Intramolecular hydrogen bond energy and cooperative interactions in α-, β-, and γ-cyclodextrin conformers

Accurate estimation of individual intramolecular hydrogen bond (H-bond) energies is an intricate task for multiply H-bonded systems. In such cases, the hydrogen bond strengths could be highly influenced by the cooperative interactions, for example, those between hydroxyl groups in sugars. In this work, we use the recently proposed molecular tailoring approach-based quantification (Deshmukh, Gadre, and Bartolotti, J Phys Chem A 2006, 110, 12519) to the extended systems of cyclodextrins (CDs). Further, the structure and stability of different conformers of α-, β-, and γ-CDs are explained based on the energetics and cooperative contribution to the strength of these H-bonds. The estimated O-H···O H-bond energies in the various CD conformers are found to vary widely from 1.1 to 8.3 kcal mol(-1). The calculated energy contributions to cooperativity toward the H-bond strengths fall in the range of 0.25-2.75 kcal mol(-1).     

Decomposition Mechanism of 5,5′-Bis(tetrazole)-1,1′-dioIate(TKX-50) Anion Initiated by Intramolecular Oxygen Transfer

Density functional theory calculations at the B3LYP/6-31+G^** and B3LYP/6-311++G ^** levels were perfonned on thermal decomposition of 5,5′-bis(tetrazole)-1 ,r-diolate(TKX-50) anion with an intramolecular oxygen transfer being an initial step. Tlie results show that the intramolecular oxygen transfers are the rate-limiting steps for the decomposition of title anion with activation energies being in the range of 287-328 kJ/mol. Judged by the nucleus- independent chemical shift values, the formation of antiaromatic ring in transition state or the decrease of aromaticity of the tetrazole ring of the reactant makes somewhat contribution to the high potential energies of the rate-limiting transition states. However, the activation energies of the following N2 elimination tlirough various pathways are in a low range of 136-166 kJ/mol. The tetrazole ring acts as an electron donor or acceptor in difierent pathways to assist the bond nipture or group elimination. The rate constants in a temperature range of 500-2000 K for all the intramolecular oxygen transferring reactions were obtained. The corresponding linear relationships between InA and 1/T were established.     

金属丝桃蒽酮结构变化的理论研究

用MMX和AM1方法对金属桃蒽酮(HYP)结构变化过程的生成热进行了计算.发现:1.HYP1,2位OH可越过20kJ/mol左右的势,绕C--O键旋转而形成分子内氢键,并估算出键能约为10kJ/mol;2.HYP其他四个OH也可进行类似的构象变化,势垒在26kJ/mol左右,相应分子内氢键键能约为20kJmol;3.HYP分子内氢传递产生的异构体在能量上不稳定,进而在基础上探讨了1,2位OH分子内氢键的形成对HYP光敏活性的影响。     

Theoretical analysis of fluoroglycine conformers

Seven different optimized conformers of α‐fluoroglycine (H₂NCHFCOOH) were obtained from ab initio calculations. Some of these conformers are exceptionally stable compared to similar conformers of glycine. Conformers in which the lone pair of electrons on the nitrogen atom are antiperiplanar to the C F bond are more stable than conformers that do not have such an arrangement. The stability difference between conformers with such an arrangement and conformers that have the lone pair of electrons synperiplanar to the C F bond is about 27 kJ/mol (calculated at the MP2/6‐31+G* level). Conformers that have the lone pair of electrons antiperiplanar to the C F bond possess a longer C F bond, a shorter C N bond, and sp²‐like amino bond angles. For some conformers an unusual hydrogen bond involving the acidic carboxylic acid hydrogen and the electronegative fluorine atom is observed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 426–431, 2000     

Infrared and Raman spectra, conformational stability, ab initio calculations, and vibrational assignments for methylaminothiophosphoryl difluoride

Infrared spectra (4000–50 cm⁻¹) of the vapor, amorphous and crystalline solids and Raman spectra (3600–10 cm⁻¹) of the liquid with qualitative depolarization data as well as the amorphous and crystalline solids of methylaminothiophosphoryl difluoride, CH₃N(H)P(=S)F₂, and three deuterated species, CD₃N(H)P(=S)F₂, CH₃N(D)P(=S)F₂, and CD₃N(D)P(=S)F₂, have been recorded. The spectra indicate that in the vapor, liquid and amorphous solid a small amount of a second conformer is present, whereas only one conformer remains in the low temperature crystalline phase. The near-infrared spectra of the vapor confirms the existence of two conformers in the gas phase. Asymmetric top contour simulation of the vapor shows that the trans conformer is the predominant vapor phase conformer. From a temperature study of the Raman spectrum of the liquid the enthalpy difference between the trans and near-cis conformers was determined to be 368±15 cm⁻¹ (4.41±0.2 kJ/mol), with the trans conformer being thermodynamically preferred. Ab Initio calculations with structure optimization using the 6-31G(d) and 6-311+G(d,p) basis sets at the restricted Hartree–Fock (RHF) and/or with full electron correlation by the perturbation method to second order (MP2) support the occurrence of near-trans (5° from trans) and near-cis (20° from cis) conformers. From the RHF/6-31G(d) calculation the near-trans conformer is predicted to be the more stable form by 451 cm⁻¹ (5.35 kJ/mol) and from the MP2/6-311+G(d,p) calculation by 387 cm⁻¹ (4.63 kJ/mol). All of the normal modes of the near-trans rotamer have been assigned based on infrared band contours, depolarization values and group frequencies and the assignment is supported by the normal coordinate calculation utilizing harmonic force constants from the MP2/6-31G(d) ab initio calculations.     

A comparative ab initio study of methyl formate, methyl thiolformate and methyl thionoformate

Ab initio SCF-MO calculations have been carried out for HCOOCH₃, HC(=O)SCH₃ and HC(=S)OCH₃. Relative stabilities of s-trans/s-cis conformers are reported and discussed in terms of specific intramolecular interactions. The energy difference between the s-trans and the s-cis form increases in the order methyl thiolformate < methyl thionoformate < methyl formate. The major stabilizing factors of the s-cis forms are the bond dipolar interaction and the mesomeric delocalization through the five member ring involving both the X=C---Y---C (X, Y = O, S) skeleton and the out-of-plane hydrogen atoms. These effects are used to explain the trends mentioned. The non-planarity previously proposed for the thionoester is reinvestigated. Our calculations show that this molecule is planar. Molecular atomic charges, dipole moments and ionisation potentials are determined and compared with available experimental values.     

Ab initio calculations on phenol–water

The structures of the three phenol–water minima are optimized with MP2 and the interaction-optimized DZPi basis set. Single point calculations are carried out using the slightly larger ESPB basis set, which contains a set of (s,p) bond functions at the midpoint of the hydrogen-bond. The binding energies and hydrogen-bond distances are corrected for basis set superposition error. For all minima, our binding energies D_e are larger than the previous theoretical estimates. Despite this, our best estimate of the binding energy D₀ for the global minimum, 21.08 kJ/mol, is about 2 kJ/mol smaller than the experimental values (23.45±0.48 and 22.92±0.36 kJ/mol).     

Structure and stability of thioureate anions with water, DFT calculations

Structure and stability of thioureate anion with the water clusters CSNH₂NH⁻-(H₂O)_n = 1–7, are studied, using density functional theory. Molecular structures and the stability of the clusters are discussed based on the calculation results of the stable conformers and their relative energies. All the clusters are stable thermodynamically in gas phase with respect to separate monomers. The clusters are stabilized progressively with an increasing number of water molecules, as indicated by the increasing of the binding energies. The binding energies of CSNH₂NH⁻ and a water molecule are 14.34 and 16.36 kcal/mol for cis CSNH₂NH⁻ and trans CSNH₂NH⁻, respectively. As the reaction in aqueous solution progresses, the CS bond distance increases monotonically, indicating that the CS bond of the thioureate anion unit in the clusters is de-stabilized with an increasing number of water molecules.