The conformers of phenylglycine

The neutral form of the unnatural amino acid phenylglycine was vaporized by laser ablation, and the presence of two conformers was detected in a supersonic expansion by Fourier transform microwave spectroscopy. Both conformers were unequivocally identified by comparison of their experimental rotational and quadrupole coupling constants with those calculated ab initio. The most stable conformer is stabilized by intramolecular hydrogen bonds N-H...O=C, N-H...pi (with the closest C-C bond in the aromatic ring), and a cis-COOH interaction. The other conformer exhibits a O-H...N hydrogen bond between the hydrogen atom of the hydroxyl group and the lone pair at the nitrogen atom.     

Uncatalyzed peptide bond formation between two double amino acid molecules in the gas phase

The gas phase mechanism for peptide bond formation between two double amino acid (DAA) molecules ((NH₂)₂C(COOH)₂) is investigated in the absence of any catalysts. Two different paths, concerted and stepwise, each leading to both cis and trans DAA‐DAA dipeptide products (four mechanisms total) are examined on the basis of theoretical calculations carried out at the CCSD(T)/aug‐cc‐pVDZ//MP2/aug‐cc‐pVDZ level. The investigation indicates that the concerted mechanism leading to the trans configuration of the peptide bond in the DAA‐DAA dipeptide product is thermodynamically favored by about 5 kcal mol^?1 and requires slightly less energy than the remaining pathways considered. Moreover, the peptide bond formation process between two DAA molecules in the gas phase resembles the analogous reactions between two natural amino acids.     

Spectroscopic and theoretical study of vibrational spectra of hydrogen‐bonded tropolone

Theoretical simulation of the bandshape and fine structure of the ν_s stretching band is presented for tropolone‐H and tropolone‐D taking into account an adiabatic coupling between the high‐frequency O–H(D) stretching and the low‐frequency intra‐ and intermolecular OO stretching modes, and linear and quadratic distortions of the potential energies for the low‐frequency vibrations in the excited state of the O–H(D) stretching vibration. In order to determine the low‐frequency vibrations, the experimental spectra of the polycrystalline tropolone in the far‐infrared and the low‐frequency Raman range have been recorded for the first time. The experimental frequencies in the low‐frequency region are compared with the results of the HF/6‐31G** and Becke3LYP/6‐31G** calculations carried out for the tropolone dimer. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 275–282, 1999     

Intramolecular hydrogen bonding in structural conformers of 2‐amino methylene malonaldehyde: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energies of 44 conformers of 2‐Amino methylene malonaldehyde were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set and AIM and NBO analysis. The calculated geometrical parameters and conformational analysis in gas phase show that the closed ring via intramolecular hydrogen bonded conformers of this compound are more stable than the other ones. Hydrogen bond energies for H‐bonded conformers were obtained from the related rotamers method (RRM) and Schuster method, and also the nature of H‐bonding of them has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. Delocalization effects can be identified from the presence of off diagonal elements of the Fock matrix in the NBO basis. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Theoretical investigation of carbon-sulfur triple bonds

By means of first principle calculations we have investigated a set of molecules that are presumed to contain carbon-sulfur triple bonds, namely HCSOH, H(3)SCH, cis-FCSF, F(3)CCSF(3), and F(5)SCSF(3). For HCSOH, FCSF, and H(3)SCH we used the CCSD(T) methodology and the correlation-consistent basis sets. On the other hand, F(3)CCSF(3) and F(5)SCSF(3) were studied at the B3LYP, M06-2X, MP2, and G3 levels of theory. We found that none of these molecules display a carbon-sulfur adiabatic bond dissociation energy (ABDE) as strong as diatomic CS (170.5 kcal mol(-1)), or a diabatic bond dissociation energy (DBDE) larger than the one found in SCO (212.0 kcal mol(-1)), although the DBDE of FCSF comes quite close at 208.3 kcal mol(-1). The CS ABDEs of F(3)CCSF(3), F(5)SCSF(3), and H(3)SCH are comparable to that of a single C-S bond. In contrast with the experimental results, F(3)CCSF(3) and F(5)SCSF(3) are predicted to be linear with C(3v) and C(s) symmetry, respectively, at the B3LYP/6-311+G(3df,2p) level. MP2/6-311+G(2df,2p) calculations support the C(3v) symmetry for F(3)CCSF(3), despite F(5)SCSF(3) not having a perfect linear structure; the CSC angle is 174.6°, which is nearly 20° larger than the experimental value. The analysis of the carbene structures of HCSOH and H(3)SCH revealed that they are not significant, because the triplet state is dissociative in these cases. However, for F(3)CCSF(3) and F(5)SCSF(3) , the carbene triplet states lie 0.81 and 0.77 eV above the singlet state, respectively. In the same vein, our investigation supports the presence of a strong double bond for HCSOH. The conflicting evidence available for F(3)CCSF(3) and F(5)SCSF(3) makes it very difficult to determine the nature of the CS bonds. However, the bond dissociation energies and the singlet-triplet splittings clearly suggest that these compounds should be considered as masked sulfinylcarbenes. The analysis of the bond dissociation energies challenges the existence of a triple bond in these five molecules, but from a strictly thermodynamic standpoint, cis-FCSF is found to be the candidate most likely to exhibit triple-bond character.     

Theoretical insights into the mechanism of acetylcholinesterase-catalyzed acylation of acetylcholine

Acylation of acetylcholine (ACh) catalyzed by acetylcholinesterase (AChE) has been studied using high-level theoretical calculations on a model system that mimics the reaction center of the enzyme, and compared with uncatalyzed acylation reaction. The geometries of all the intermediates and transition states, activation energies, and solvent effects have been calculated. The calculations predict simultaneous formation of two short-strong hydrogen bonds (SSHB) in the rate-determining transition state structures [the first SSHB involves the hydrogen atom of Ser-200 (H(s)) and another involves the hydrogen atom of His-440 (H(h))]. In the intermediate states, the H-bond corresponding to H(h) involves SSHB, whereas the one corresponding to H(s) does not.     

Rapid Prediction of the Hydrogen Bond Cooperativity in N‐methylacetamide Chains

A method is proposed to rapidly predict the hydrogen bond cooperativity in N‐methylacetamide chains. The parameters needed are obtained from the fittings to the hydrogen bonding energies in the formamide chains containing 2 to 8 monomeric units. The scheme is then used to calculate the individual hydrogen bonding energies in N‐methylacetamide chains containing 2 to 7 monomeric units. The cooperativity predicted is in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction. Our scheme is further employed to predict the individual hydrogen bonding energies in larger N‐methylacetamide chains containing up to 200 monomeric N‐methylacetamide units, to which the MP2 method cannot be applied. Based on our scheme, a cooperative effect of over 170 % of the dimer hydrogen bonding energy in long N‐methylacetamide chains is predicted. The method is also applied to heterogeneous chains containing formamide, acetamide, N‐methylformamide, and N‐methylacetamide. The individual hydrogen bonding energies in these heterogeneous chains are also in good agreement with those obtained from MP2 calculations with the BSSE correction, further demonstrating that our method is reasonable.     

Improper hydrogen C-H...O bonds cause self-association of alpha, beta-enaminoketones containing fluorosubstituted alkyl groups.

Concentration- and temperature-dependent IR, NMR and dipole-moment studies on 4-N,N-dimethylamino-1,1,1-trifluoro-3-buten-2-one and two of its higher homologues showed that these compounds undergo reversible dimerization in nonpolar solvents. Antiparallel "closed" dimers are formed with a network of improper intermolecular C-H...O hydrogen bonds. Quantitative analysis of the 1H NMR data yielded delta H0 = -17.6 kJ mol-1 and delta S0 = -46.9 J deg-1 mol-1. The interactions observed are the strongest among those involving a C-H group reported so far. The complex described here is the first example of a cyclic complex stabilized by two improper C-H...O hydrogen bonds. The conclusions drawn from the solution and solid-state data were confirmed by ab initio calculations.     

Hydrogen bonding in acetylacetaldehyde: Theoretical insights from the theory of atoms in molecules

All the possible conformations of tautomeric structures (keto and enol) of acetylacetaldehyde (AAD) were fully optimized at HF, B3LYP, and MP2 levels with 6‐31G(d,p) and 6‐311++G(d,p) basis sets to determine the conformational equilibrium. Theoretical results show that two chelated enol forms have extra stability with respect to the other conformers, but identification of global minimum is very difficult. The high level ab initio calculations G2(MP2) and CBS‐QB3) also support the HF conclusion. It seems that the chelated enol forms have equal stability, and the energy gap between them is probably lies in the computational error range. Finally, the analysis of hydrogen bond in these molecules by quantum theory of atoms in molecules (AIM) and natural bond orbital (NBO) methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Theoretical study of the intermolecular hydrogen bond interaction for furan-HCl and furan-CHCl_3 complexes

The importance of intermolecular interactions in biology and material science has prompted chemists to explore the nature of the variety of such interactions. The strongest of these interac-tions are the hydrogen bonds, which play an important role in determining the molecular confor-mation, crystal packing, and the structure of biological systems such as nucleic acids. Extensive experimental and theoretical efforts[1—5] have been devoted to the studies of this type of interac-tions, such as …     

Geometrical consequences of resonance-assisted intramolecular hydrogen-bond formation from Ab initio MO calculations on 2-nitroresorcinol

Ab initio orbital calculations on phenol, nitrobenzene, and 2-nitroresorcinol have been performed with the GAUSSIAN 92 series of programs. Initial RHF/6-31G^* and RHF/6-31G^** optimizations were followed by second-order MØller-Plesset MP2(FC)/6-31G^* optimizations. The general geometrical features of these molecules, and, in particular, the characteristic changes as going from phenol to 2-nitroresorcinol and from nitrobenzene to 2-nitroresorcinol are in good agreement with recent gas-phase electron diffraction studies and with the notion of resonance-assisted intramolecular hydrogen-bond formation in 2-nitroresorcinol.     

Theoretical evidence for pyramidalized bicyclic serine enolates in highly diastereoselective alkylations

A new chiral serine equivalent and its enantiomer have been synthesized from (S)- and (R)-N-Boc-serine methyl esters (Boc: tert-butyloxycarbonyl). The use of these compounds as chiral building blocks has been demonstrated in the synthesis of alpha-alkyl alpha-amino acids by diastereoselective potassium enolate alkylation reactions and subsequent acid hydrolyses. Theoretical studies were performed to elucidate the stereochemical outcome of both the formation of five-membered cyclic N,O-acetals and the subsequent alkylation process, which occurs with total retention of configuration. This feature could be explained in terms of the high degree of pyramidalization of enolate intermediates.     

Interaction of carboranes with biomolecules: formation of dihydrogen bonds.

Noncovalent interactions of the polyhedral carborane 1-carba-closo-dodecaborane (CB(11)H(12))(-) with building blocks of biomolecules, modelled by glycine (GLY), serine (SER), phenylalanine (PHE), glutamic acid (GLU), lysine (LYS) and arginine (ARG), were investigated in vacuo by molecular dynamics simulations with the UFF empirical potential. Selected structures were further studied by accurate ab initio quantum chemical procedures. Interactions with a peptide bond (GLY-SER dipeptide) and a nucleic acid building block (guanine) were also considered. The RESP and NPA charges of carboranes and small model systems are compared and their use is discussed. The dominant interaction between carboranes and biomolecules is the formation of unconventional proton-hydride hydrogen bonds (dihydrogen bonds) characterized by a short distance between hydrogen atoms (as close as 1.8 A) and an average strength in the range of 4.2-5.8 kcal mol(-1). The total stabilization energy of complexes investigated is rather large, and the largest value (approximately 15 kcal mol(-1)) was found for the carborane complexes with ARG and the GLY-SER dipeptide. These interactions are ubiquitous under geometrical constraints influencing the strength of the interaction. The carborane forms dihydrogen bonds with biomolecules preferably with the hydrogen atoms of its lower hemisphere (i.e. the part of the cage opposite to the carbon atom). These two geometrical factors can be used to explain the specificity of inhibition of HIV protease by carboranes.     

Theoretical investigations into the blue-shifting hydrogen bond in benzene complexes.

The benzene...X complexes (X=benzene, antracene, ovalene) were optimised at the MP2/6-31G** level with the C2v symmetry of the complex and planarity of the proton acceptor being preserved. The resulting stabilisation energies amount to 1.2, 2.3 and 2.9 kcal mol(-1), and the C-H bond of the proton donor is contracted by 0.0035, 0.0052 and 0.0055 A, respectively. The contraction is connected with a blue-shift of the C-H stretch vibration frequency. A two-dimensional anharmonic vibration treatment based on a MP2/6-31G** potential energy surface yields the following blue shifts for the complexes studied: 28, 42 and 43 cm(-1). The dominant attraction in the complexes is London dispersion, while the attractive contribution from electrostatic quadrupole-quadrupole interactions is considerably smaller.     

Comparative study on formamide–water complex

The hydrogen bonding of 1:1 complexes formed between formamide and water molecule have been investigated systematically using Hartree–Fock (HF), hybrid density functional theory (B3LYP), and post‐Hartree–Fock (MP2 and CCSD(T)) methods with range of basis sets 6‐31G(d), cc‐pVXZ (X = D, T, Q) and aug‐cc‐pVYZ (Y = D, T). Three stable structures are considered on the potential energy surface of formamide and water system. The optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The IR frequencies, intensities, and frequency shifts are reported. This study shows that B3LYP/aug‐cc‐pVDZ method gives better performance for formamide‐water complexes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010.     

Theoretical characterization of the gas-phase O(3)HO hydrogen-bonded complex.

We report a theoretical study on two gas-phase hydrogen-bonded complexes formed between ozone and hydroxyl radical that have relevance to atmospheric chemistry. This study was carried out by using CASSCF, CASPT2, QCISD, and CCSD(T) theoretical approaches in conjunction with the 6-311+G(2df,2p) and aug-cc-pVTZ basis sets. Both complexes have a planar structure and differ from each other in the orientation of the electronic density of the unpaired electron associated with the HO radical moiety. Our calculations predict their stabilities to be 0.87 and 0.67 kcal mol(-1), respectively, at 0 K and show the importance of anharmonic effects in computing the red shift of the HO stretch originating from the hydrogen-bonding interaction. We also report two transition states involving the movement of the HO moiety on the potential energy surfaces of these hydrogen-bonded complexes.     

Ab initio investigation of water clusters (H2O)n (n = 2–34)

Various properties of typical structures of water clusters in the n = 2–34 size regime with the change of cluster size have been systematically explored. Full optimizations are carried out for the structures presented in this article at the Hartree–Fock (HF) level using the 6‐31G(d) basis set by taking into account the positions of all atoms within the cluster. The influence of the HF level on the results has been reflected by the comparison between the binding energies of (H₂O)_n (n = 2–6, 8, 11, 13, 20) calculated at the HF level and those obtained from high‐level ab initio calculations at the second‐order Møller–Plesset (MP2) perturbation theory and the coupled cluster method including singles and doubles with perturbative triples (CCSD(T)) levels. HF is inaccurate when compared with MP2 and CCSD(T), but it is more practical and allows us to study larger systems. The computed properties characterizing water clusters (H₂O)_n (n = 2–34) include optimal structures, structural parameters, binding energies, hydrogen bonds, charge distributions, dipole moments, and so on. When the cluster size increases, trends of the above various properties have been presented to provide important reference for understanding and describing the nature of the hydrogen bond. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Analysis of Proton NMR in Hydrogen Bonds in Terms of Lone‐Pair and Bond Orbital Contributions

NMR spectroscopic parameters of the proton involved in hydrogen bonding are studied theoretically. The set of molecules includes systems with internal resonance‐assisted hydrogen bonds, internal hydrogen bonds but no resonance stabilization, the acetic acid dimer (AAD), a DNA base pair, and the hydrogen succinate anion (HSA). Ethanol and guanine represent reference molecules without hydrogen bonding. The calculations are based on zero‐point vibrationally averaged molecular structures in order to include anharmonicity effects in the NMR parameters. An analysis of the calculated NMR shielding and J‐coupling is performed in terms of “chemist’s orbitals”, that is, localized molecular orbitals (LMOs) representing lone‐pairs, atomic cores, and bonds. The LMO analysis associates some of the strong de‐shielding of the protons in resonance‐assisted hydrogen bonds with delocalization involving the π‐backbone. Resonance is also shown to be an important factor causing de‐shielding of the OH protons for AAD and HSA, but not for the DNA base pair. Nitromalonamide (NMA) and HSA have particularly strong hydrogen bonds exhibiting signs of covalency in the associated J‐couplings. The analysis results show how NMR spectroscopic parameters that are characteristic for hydrogen bonded protons are influenced by the geometry and degree of covalency of the hydrogen bond as well as intra‐ and intermolecular resonance.