Glycine Dimers: Structure,Stability, and Medium Effects

We report a study on different ionization states and conformations of the bimolecular (Gly)₂ system by means of quantum mechanical calculations. Optimized geometries for energy minima of the glycine dimer, as well as relative energies and free energies were computed as a function of the medium: gas phase, nonpolar polarizable solvent, and aqueous solution. The polarizable continuum model was employed to account for solvation effects. Energy calculations were done using the MP2/aug‐cc‐pVTZ and B3LYP/6‐311+G(2df,2p) methods on B3LYP/6‐31+G(d,p) optimized structures (some single‐point energy calculations were also done using the B3PW91 and PBE1KCIS methods). Ionized forms of the glycine dimer (either zwitterion–zwitterion or neutral–zwitterion) are predicted to exist in all media, in contrast to amino acid monomers. In aqueous solution, dimerization is an exergonic process (?4 kcal mol^?1). Thus, according to our results, zwitterion–zwitterion Gly dimers might be abundant in supersaturated glycine aqueous solutions, a fact that has been connected with the structure of α‐glycine crystals but that remains controversial in the literature. Another noticeable result is that zwitterion–zwitterion interactions are substantially underestimated when computed using methods based on density functional theory. For comparison, some calculations for the dimer of the simplest chiral amino acid alanine were done as well and differences to the glycine dimer are discussed.     

An ab initio study of the structure,dissociation energy,and heat of formation of Na2S

The equilibrium geometries and fundamental frequencies of Na₂S are calculated at HF, MP2(FC, FU), and MP3 with the 6–31G(d) basis set and at HF and MP2(FC, FU) with the 6–31G(d) basis set, respectively. The total energy at MP2(FU)/6–31G(d)-optimized geometry is computed at MP4 with 6–311G(d, p), 6–311 + G(d, p), and 6–311G(2df, p), at QCISD(T)/6–311G(d, p), and at MP2/6–311G(3df, 2p) levels, respectively. The dissociation energy, the atomization energy, and the heat of formation for Na₂S are evaluated using the G1 and G2 models. The calculated results indicated that Na₂S in its ground state was a bent structure (C_2v). Electron correlation corrections on the bending angle are very significant. The equilibrium geometrical parameters are R_e(Na-S) = 2.45 Å and ∠Na-S-Na = 111.13° at the MP2(FU)/6–31G(d) level. The theoretically estimated dissociation energy, total atomization energy, and heat of formation are 67.07, 117.55, and 0.35 kcal mol⁻¹, respectively, at 298.15 K. © 1997 John Wiley & Sons, Inc.     

复合物HNO···H2O2内N-H···O蓝移氢键的理论研究

A theoretical study on the blue-shifted H-bond N-H…O and red-shifted H-bond O-H…O in the complexHNO…H_2O_2 was conducted by employment of both standard and counterpoise-corrected methods to calculate thegeometric structures and vibrational frequencies at the MP2/6-31G(d),MP2/6-31 G(d,p),MP2/6-311 q G(d,p),B3LYP/6-31G(d),B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels.In the H-bond N-H…O,the calcu-lated blue shift of N-H stretching frequency is in the vicinity of 120 cm~(-1) and this is indeed the largest theoreticalestimate of a blue shift in the X-H…Y H-bond ever reported in the literature.From the natural bond orbital analy-sis,the red-shifted H-bond O-H…O can be explained on the basis of the dominant role of the hyperconjugation.For the blue-shifted H-bond N-H…O,the hyperconjugation was inhibited due to the existence of significant elec-tron density redistribution effect,and the large blue shift of the N-H stretching frequency was prominently due tothe rehybridization of sp~n N-H hybrid orbital.     

On the additivity of basis set effects in some simple fluorine containing systems

The reactions F + H₂ → HF + H, HF → H + F, F → F⁺ + e^? and F + e^? → F^? were used as simple test cases to assess the additivity of basis set effects on reaction energetics computed at the MP4 level. The 6-31G and 6-311G basis sets were augmented with 1, 2, and 3 sets of polarization functions, higher angular momentum polarization functions, and diffuse functions (27 basis sets from 6-31Gd, p) to 6-31 ++ G(3df, 3pd) and likewise for the 6-311G series). For both series substantial nonadditivity was found between diffuse functions on the heavy atom and multiple polarization functions (e.g., 6-31 + G(3d, 3p) vs. 6-31 + G(d, p) and 6-31G(3d, 3p)). For the 6-311G series there is an extra nonadditivity between d functions on hydrogen and multiple polarization functions. Provided that these interactions are taken into account, the remaining basis set effects are additive to within ±0.5 kcal/mol for the reactions considered. Large basis set MP4 calculations can also be estimated to within ±0.5 kcal/mol using MP2 calculations, est. E_MP4(6-31 ++ G(3df, 3pd)) ≈ E_MP4(6-31G(d, p)) + E_MP2(6-31 ++ G(3df, 3pd)) – E_MP2(6-31G(d, p)) or E_MP4(6-31 + G(d, p) + E_MP2(6-31 ++ G(3df, 3pd)) – E_MP2(6-31 + G(d, p)) and likewise for the 6-311G series.     

A quantum mechanical approach to the kinetics of the hydrogen abstraction reaction H2O2 + •OH → HO2 + H2O

The kinetics of the hydrogen abstraction from H₂O₂ by ^?OH has been modeled with MP2/6‐31G*//MP2/6‐31G*, MP2‐SAC//MP2/6‐31G*, MP2/6‐31+G**//MP2/6‐31+G**, MP2‐SAC// MP2/6‐31+G**, MP4(SDTQ)/6‐311G**//MP2/6‐31G*, CCSD(T)/6‐31G*//CCSD(T)/6‐31G*, CCSD(T)/6‐31G**//CCSD(T)/6‐31G**, CCSD(T)/6‐311++G**//MP2/6‐31G* in the gas phase. MD simulations have been used to generate initial geometries for the stationary points along the potential energy surface for hydrogen abstraction from H₂O₂. The effective fragment potential (EFP) has been used to optimize the relevant structures in solution. Furthermore, the IEFPCM model has been used for the supermolecules generated via MD calculations. IEFPCM/MP2/6‐31G* and IEFPCM/CCSD(T)/6‐31G* calculations have also been performed for structures without explicit water molecules. Experimentally, the rate constant for hydrogen abstraction by ^?OH drops from 1.75 × 10^?12 cm³ molecule^?1 s^?1 in the gas phase to 4.48 × 10^?14 cm³ molecule^?1 s^?1 in solution. The same trend has been reproduced best with MP4 (SDTQ)/6‐311G**//MP2/6‐31G* in the gas phase (0.415 × 10^?12 cm³ molecule^?1 s^?1) and with EFP (UHF/6‐31G*) in solution (3.23 × 10^?14 cm³ molecule^?1 s^?1). © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 502–514, 2005     

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     

Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations

The interaction of Zn²⁺ with glycine (Gly) in the gas phase is studied by a combination of ab initio and molecular mechanics techniques. The structures and energetics of the various isomers of the Gly–Zn²⁺ complex are first established via high‐level ab initio calculations. Two low‐energy isomers are characterized: one in which the metal ion interacts with the carboxylate end of zwitterionic glycine, and another in which it chelates the amino nitrogen and the carbonyl oygen of neutral glycine. These calculations lead to the first accurate value of the gas‐phase affinity of glycine for Zn²⁺. Ab initio calculations were also used to evaluate the performance of various implementations of the SIBFA force field. To assess the extent of transferability of the distributed multipoles and polarizabilities used in the SIBFA computations, two approaches are followed. In the first, approach (a), these quantities are extracted from the ab initio Hartree–Fock wave functions of glycine or its zwitterion in its entirety, and for each individual Zn²⁺‐binding conformation. In the second, approach (b), they are assembled from the appropriate constitutive fragments, namely methylamine and formic acid for neutral glycine, and protonated methylamine and formate for the zwitterion; they undergo the appropriate vector or matrix rotation to be assembled in the conformation studied. The values of the Zn²⁺–glycine interaction energies are compared to those resulting from ab initio SCF and MP2 computations using both the all‐electron 6‐311+G(2d,2p) basis set and an effective core potential together with the valence CEP 4‐31G(2d) basis set. Approach (a) values closely reproduce the ab initio ones, both in terms of the total interaction energies and of the individual components. Approach (b) can provide a similar match to ab initio interaction energies as does approach (a), provided that the two constitutive Gly building blocks are considered as separate entities having mutual interactions that are computed simultaneously with those occurring with Zn²⁺. Thus, the supermolecule is treated as a three‐body rather than a two‐body system. These results indicate that the current implementation of the SIBFA force field should be adequate to undertake accurate studies on zinc metallopeptides. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 963–973, 2000     

Chemical Reactivity of Oxo‐ and Aza‐γ‐lactam Rings

Different mechanisms for the alkaline hydrolysis of oxo and aza‐γ‐lactam rings have been studied by ab initio calculations at the MP2/6‐31+G*//MP2/6‐31+G* and B3LYP/6‐31+G*//B3LYP/6‐31+G* levels. The tetrahedral intermediate can undergo two different reactions, the cleavage of the C₂−N₂ bond (the classical mechanism) and the cleavage of the C₂−X₆ bond (X=O, N). Both compounds present similar energy barriers for the classical fragmentation, and show considerably lower barriers for the alternative mechanism. Because of this reactivity, the compounds studied are expected to be β‐lactamase inhibitors.     

Large amplitude oscillations of protons in water clusters

Synchronous oscillations of bridge protons in molecular rings of (H₂O) _n water clusters with n = 4–6, 8, and 12 are analyzed as large amplitude motions that result in the inversion of the hydrogen bond sequence in a single ring. The corresponding one-dimensional cross sections of the potential energy surfaces (symmetric double-well potentials) are constructed at the MP2/6–31++G(d, p) level. The eigenstates of the systems in the constructed potentials in the energy range up to the top of the barrier are determined. The synchronous oscillations of protons are shown to be coupled to vibrations of the oxygen skeleton of the molecular ring, and the typical frequencies of the complex vibrations lie in the range of 230–330 cm^?1.     

NMR chemical shielding and spin–spin coupling constants across hydrogen bonds in uracil–α-hydroxy-N-nitrosamine complexes

One- and two bond spin–spin coupling constants, ¹ J, ^1h J , and ^2h J across X–H?O hydrogen bonds and shielding constants of bridging hydrogens have been computed for complexes formed from interaction between the α-hydroxy-N-nitrosamine (NP) and four preferential binding sites of the uracil (U) at B3LYP/6-311++G(2d,2p)//MP2/6-311++G(2d,2p) level of theory. All complexes are stabilized by two H_U?O_NP and H_NP?O_U hydrogen bonds. Very good correlations were found between NMR spin–spin coupling constant as well as isotropic shielding constant and the binding energy, H-bond distance, red-shift of vibration frequency, charge transfer energy, and electron density at H-bond critical point.     

Searching blue-shifted O–H···Y hydrogen bond in CH<Subscript>3</Subscript>OH complexes with CF<Subscript>4</Subscript>, C<Subscript>2</Subscript>F<Subscript>2</Subscript>, OC,Ne, and He: a theoretical study

The hydrogen-bonded structures of the CH₃OH complexes with CF₄, C₂F₂, OC, Ne, and He are designated as the starting points for geometry optimizations without and with counterpoise (CP) correction at MP2 level of theory with the basis sets 6-31+G*, 6-31++G**, and 6-311++G**, respectively. Tight convergence criteria are applied throughout all geometry optimizations in order to reduce the computational errors. According to the optimizations without CP correction, a blue-shifted O–H···Y (where Y = F, O, Ne, or He) hydrogen bond exists in all these five complexes. The magnitudes of blue shifts of ν(O–H) of the former four complexes with respect to that of CH₃OH are reduced greatly when the polarization and diffuse functions of the hydrogen atoms are added (results from 6-31+G* versus those from 6-31++G**). However, for the complexes CH₃OH–CF₄ and CH₃OH–C₂F₂, our optimizations using the CP corrections did not find the hydrogen-bonded structure to be a stationary point. The energy minimum of both the complexes corresponds to a non-hydrogen-bonded structure.     

The competition between the intramolecular hydrogen bond and π‐electron delocalization in trifluoroacetylacetone—A theoretical study

Conformational study of trifluoroacetylacetone was carried out using the HF, B3LYP, and MP2 methods with the 6‐31G(d, p) and 6‐311++G(d, p) basis sets. All of the results show that the chelated enol structures (E11 and E31) have extra stability with respect to the other forms and one of them (E11) is global minimum. The energy gap between the chelated forms is in the range 0.7–5.9 kJ mol^?1. Theoretical calculations show that this compound has an asymmetric double minimum potential energy surface which is in contrast with the electron diffraction result. Moreover, the computational results predict that due to the withdrawing effect of CF₃ group, hydrogen bond in trifluoroacetylacetone is weaker than the acetylacetone. Because of the more stability of E11, it is expected that the hydrogen bond energy in E11 is greater than the E31, but at all of the computational levels with most extended basis set the converse results were observed. These results clearly show that the hydrogen bond is not a superior parameter in conformational preference and the contribution of resonance is probably greater than the hydrogen bond. Finally, the analysis of this system by quantum theory of atoms in molecules and natural bond orbital methods fairly support the ab initio results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

A Comparison of the Interacting Quantum Atoms (IQA) Analysis of the Two-Particle Density-Matrices of MP4SDQ and CCSD

Within the quantum topological energy partitioning method called Interacting Quantum Atoms (IQA) we transition from Møller-Plesset (MP4SDQ) to CCSD in calculating intra- and interatomic electron correlation energies for a set of hydrides, diatomics, a few simple molecules and non-covalently bonded complexes, using the uncontracted basis set 6-31++G(2d,2p). CCSD-IQA allows a more rigorous analysis of atomic electron correlation than that offered by Møller-Plesset, which returns IQA contributions that are identical to Hartree–Fock counterparts except for two-electron terms. The CCSD-IQA analysis returns bond and other interatomic correlation energies that are typically much larger in magnitude than the MP4SDQ values. Crisp patterns of energy transferability are detected in water clusters, both for intra-atomic and interatomic correlation energies. CCSD determines that the intra-atomic correlation energy of an oxygen drops by 15 kJ · mol^–1 for donating a hydrogen and by 25 kJ · mol^–1 for accepting a hydrogen.     

Rate coefficients of the CF3CHFCF3 + H → CF3CFCF3 + H2 reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths

The minimum energy path (MEP) of the reaction, CF₃CHFCF₃ + H → transition state (TS) → CF₃CFCF₃ + H₂, has been computed at different ab initio levels and with density functional theory (DFT) using different functionals. The computed B3LYP/6‐31++G**, BH&HLYP/cc‐pVDZ, BMK/6‐31++G**, M05/6‐31+G**, M05‐2X/6‐31+G**, UMP2/6‐31++G**, PUMP2/6‐31++G**//UMP2/6‐31++G**, RCCSD(T)/aug‐cc‐pVDZ//UMP2/6‐31++G**, RCCSD(T)/aug‐cc‐pVTZ(spd,sp)//UMP2//6‐31++G**, RCCSD(T)/CBS//M05/6‐31+G**, and RCCSD(T)/CBS//UMP2/6‐31++G** MEPs, and associated gradients and Hessians, were used in reaction rate coefficient calculations based on the transition state theory (TST). Reaction rate coefficients were computed between 300 and 1500 K at various levels of TST, which include conventional TST, canonical variational TST (CVT) and improved CVT (ICVT), and with different tunneling corrections, namely, Wigner, zero‐curvature, and small‐curvature (SCT). The computed rate coefficients obtained at different ab initio, DFT and TST levels are compared with experimental values available in the 1000–1200 K temperature range. Based on the rate coefficients computed at the ICVT/SCT level, the highest TST level used in this study, the BH&HLYP functional performs best among all the functionals used, while the RCCSD(T)/CBS//MP2/6‐31++G** level is the best among all the ab initio levels used. Comparing computed reaction rate coefficients obtained at different levels of theory shows that, the computed barrier height has the strongest effect on the computed reaction rate coefficients as expected. Variational effects on the computed rate coefficients are found to be negligibly small. Although tunneling effects are relatively small at high temperatures (～1500 K), SCT corrections are significant at low temperatures (～300 K), and both barrier heights and the magnitudes of the imaginary frequencies affect SCT corrections. © 2012 Wiley Periodicals, Inc.     

Eclipsed and staggered conformations of (SIH3)2F+: An ab initio study

Ab initio calculations at 6–31G**, 6–31++G**, and MP2/6–31G** levels were performed on disilyl–fluoronium, (SiH₃)₂F⁺, with the SiH₃ group eclipsed or staggered. Optimized geometries, total energies, dipole moments, atomic charges, electronic density, and vibrational frequencies were computed. The results were compared with calculated structural parameters and vibrational frequencies of H₃SiF, H₂SiF⁺, H₂SiF^?, and H₄SiF⁺ ions. The basis-set effects were studied. Several thermochemistry parameters—ZPE, thermal energy, rotational constants, and entropies—were also calculated. © 1994 John Wiley & Sons, Inc.     

Conformers of gaseous protonated glycine

Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller–Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH₃⁺ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)₂⁺. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0–10 and 30–40 kcal mol⁻¹. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1862–1876, 1998     

Comparison of ab initio and density functional methods for vibrational analysis of TeCl4

Vibrational analysis of tellurium tetrachloride, TeCl₄, was performed with Hartree–Fock (HF), MP2, and generalized gradient approximation density functional theory (DFT) methods supplemented with polarized double-zeta split valence (DZVP) basis sets and relativistic effective core potentials (RECP) of Hay and Wadt. The molecular geometry is best reproduced at the HF and MP2/RECP+DZVP [polarized Hay and Wadt RECP for Te and 6–31G(d) basis set for Cl] levels of theory. The DFT methods gave rise to poorer results, especially those using Becke's 1988 exchange functional. Generally, the vibrational frequencies calculated by the MP2 and B3-type DFT methods with the all electron and RECP+DZVP basis sets as well as at the HF/RECP level were in satisfactory accord with the experimental data. The agreement was good enough to assist the assignment of the measured vibrational spectra. The best agreement with the experimental vibrational frequencies was achieved with the scaled HF/RECP force field. Consistent results were obtained for the unobserved A₂ (ν₄) fundamental, where the results of the best methods were within 4 cm⁻¹. The best force fields were obtained with the following methods: Becke3–Lee–Yang–Parr and Becke3–Perdew/all electron basis, MP2 and Becke3-Perdew/RECP+DZVP, and HF/RECP. The methods using RECPs are advantageous for large-scale computations. The RECP basis set effectively compensates the errors of the HF method for TeCl₄; however, it provides poor results with correlated methods. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 308–318, 1998     

Ab Initio Calculations of Structure and Energetics of the Hypermetalated Hydrogen Oxide Molecules: Li2NaOH and LiNa2OH

We made ab initio electronic calculations of the structure and energetics of mixed hypermetalated hydrogen oxides, Li₂NaOH and LiNa₂OH. There exist five equilibrium geometries for each complex. In all levels of calculation the global minimum structure for Li₂NaOH has C_2v symmetry and a large distance between sodium and oxygen, 4.24 Å (MP2/6-31G*). The dissociation energies to all possible products were also calculated. Li₂NaOH → Na + Li₂OH δH = +25.33 kcal/mol (at MP4/6-311++G**//6-31G* + ZPE scaled by 0.9). All other dissociation processes are highly endothermic. Similar procedures were applied to LiNa₂OH. The global minimum structure for LiNa₂OH belongs to point group C_s. It is also endothermic to all possible dissociation paths. LiNa₂OH →Na + LiNaOH δH = +12.72 kcal/mol (at MP4/6-311++G*//6-31G* + ZPE scaled by 0.9). The nuclear repulsion energy is crucial in energetics of the structures. The distribution of electron density and bonding properties for these equilibrium structures were analyzed.     

Cooperative enhancement of water binding to antiparallel β‐sheet models: Analysis by ab initio calculations

The cooperative enhancement of water binding to the antiparallel β‐sheet models has been studied by quantum chemical calculations at the MP2/6‐311++G**//MP2/6‐31G* level. The binding energies of the two antiparallel β‐sheet models consisting of two strands of diglypeptide are calculated by supermolecular approach. Then water molecules are gradually bonded to the diglypeptide by N? H···OH₂ and C?O···HOH hydrogen bonds. Our calculation results indicated that the hydrogen bond length and the atom charge distribution are affected by the addition of H₂O molecules. The binding energy of antiparallel diglypeptide β‐sheet models has a great improvement by the increasing of the hydrogen bond cooperativity and the more H₂O molecules added the more cooperativity enhancement can be found. The orbital interactions are calculated by natural bond orbital analysis, and the results indicate that the cooperative enhancement is closely related to the orbital interaction. © 2012 Wiley Periodicals, Inc.     

Substituent effect on intramolecular hydrogen bonding in 2‐hydroxybenzaldehyde

The effect of some substituents on intramolecular hydrogen bonding of 5‐X‐2‐hydroxybenzaldehyde (5‐X‐2‐HBA) has been studied by B3LYP and MP2 methods using 6‐311++G** and AUG‐cc‐PVTZ basis sets. The relationship between hydrogen bond energy E_HB and electron donation (or withdrawal) of substituents has been investigated. An approximately good linear relationship has been detected between Hammett coefficients and hydrogen bond formation energy (R² = 0.98). Herein, population analysis has been performed by atoms in molecules (AIM) and natural bond orbital (NBO) methods. The results of AIM and NBO analyses are in a good agreement with calculated energy values. Furthermore, correlation between ring aromaticity and hydrogen bonding has been investigated by nucleus‐independent chemical shift (NICS) at GIAO/B3LYP/6‐311++G** level of theory. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009