Noncovalent interactions of Cu+ with N-donor ligands (pyridine, 4,4-dipyridyl, 2,2-dipyridyl, and 1,10-phenanthroline): collision-induced dissociation and theoretical studies

Collision-induced dissociation of complexes of Cu+ bound to a variety of N-donor ligands (N-L) with Xe is studied using guided ion beam tandem mass spectrometry. The N-L ligands examined include pyridine, 4,4-dipyridyl, 2,2-dipyridyl, and 1,10-phenanthroline. In all cases, the primary and lowest-energy dissociation channel observed corresponds to the endothermic loss of a single intact N-L ligand. Sequential dissociation of additional N-L ligands is observed at elevated energies for the pyridine and 4,4-dipyridyl complexes containing more than one ligand. Ligand exchange processes to produce Cu+Xe are also observed as minor reaction pathways in several systems. The primary cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level are performed to obtain model structures, vibrational frequencies, and rotational constants for the neutral N-L ligands and the Cu+(N-L)x complexes. The relative stabilities of the various conformations of these N-L ligands and Cu+(N-L)x complexes as well as theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) level of theory using B3LYP/6-31G* optimized geometries. Excellent agreement between theory and experiment is observed for all complexes containing one or two N-L ligands, while theory systematically underestimates the strength of binding for complexes containing more than two N-L ligands. The ground-state structures of these complexes and the trends in the sequential BDEs are explained in terms of stabilization gained from sd-hybridization and repulsive ligand-ligand interactions. The nature of the binding interactions in the Cu+(N-L)x complexes are examined via natural bond orbital analyses.     

Noncovalent interactions of Zn+ with N-donor ligands (pyridine, 4,4'-dipyridyl, 2,2'-dipyridyl, and 1,10-phenanthroline): collision-induced dissociation and theoretical studies

The binding interactions in complexes of Zn(+) with nitrogen donor ligands, (N-L) = pyridine (x = 1-4), 4,4'-dipyridyl (x = 1-3), 2,2'-dipyridyl (x = 1-2), and 1,10-phenanthroline (x = 1-2), are examined in detail. The bond dissociation energies (BDEs) for loss of an intact ligand from the Zn(+)(N-L)(x) complexes are reported. Experimental BDEs are obtained from thermochemical analyses of the threshold regions of the collision-induced dissociation cross sections of Zn(+)(N-L)(x) complexes. Density functional theory calculations at the B3LYP/6-31G* level of theory are performed to determine stable structures of these species and to provide molecular parameters needed for the thermochemical analysis of experimental data. Relative stabilities of the various conformations of these N-donor ligands and their complexes to Zn(+) as well as theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) and M06/6-311+G(2d,2p) levels of theory using the B3LYP/6-31G* optimized geometries. The experimental BDEs for the Zn(+)(N-L)(x) complexes are in reasonably good agreement with values derived from density functional theory calculations. BDEs derived from M06 calculations provide better agreement with the measured values than those based on B3LYP calculations. Trends in the sequential BDEs are explained in terms of sp polarization of Zn(+) and repulsive ligand-ligand interactions. Comparisons are made to the analogous Cu(+)(N-L)(x) and Ni(+)(N-L)(x) complexes previously studied.     

Solvation of copper ions by acetone. structures and sequential binding energies of Cu+(acetone)x,x = 1-4 from collision-induced dissociation and theoretical studies

Collision-induced dissociation of Cu+(acetone)(x), x = 1-4, with Xe is studied as a function of kinetic energy using guided ion beam mass spectrometry. In all cases, the primary and lowest energy dissociation channel observed is endothermic loss of one acetone molecule. The primary cross section thresholds are interpreted to yield 0 and 298 K bond energies after accounting for the effects of multiple ion-neutral collisions, internal energy of the complexes, and dissociation lifetimes. Density functional calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes and provide molecular constants necessary for the thermodynamic analysis of the experimental data. Theoretical bond dissociation energies are determined from single point calculations at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels, using the B3LYP/6-31G* optimized geometries. The experimental bond energies determined here are in good agreement with previous experimental measurements made in a high-pressure mass spectrometer for the sum of the first and second bond energy (i.e., Cu+(acetone)2 --> Cu+ + 2 acetone) when these results are properly anchored. The agreement between theory and experiment is reasonable in all cases, but varies both with the size of the cluster and the level of theory employed. B3LYP does an excellent job for the x = 1 and 3 clusters, but is systematically low for the x = 2 and 4 clusters such that the overall trends in sequential binding energies are not parallel. In contrast, all MP2 values are somewhat low, but the overall trends parallel the measured values for all clusters. The trends in the measured Cu+(acetone), binding energies are explained in terms of 4s-3d sigma hybridization effects and ligand-ligand repulsion in the clusters.     

A simple model for metal cation-phosphate interactions in nucleic acids in the gas phase: Alkali metal cations and trimethyl phosphate

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations to trimethyl phosphate, TMP. Endothermic loss of the intact TMP ligand is the only dissociation pathway observed for all complexes. Theoretical calculations at the B3LYP/6-31G* level of theory are used to determine the structures, vibrational frequencies, and rotational constants of neutral TMP and the M+(TMP) complexes. Theoretical BDEs are determined from single point energy calculations at the B3LYP/6-311+G(2d,2p) level using the B3LYP/6-31G* optimized geometries. The agreement between theory and experiment is reasonably good for all complexes except Li+(TMP). The absolute M+-(TMP) BDEs are found to decrease monotonically as the size of the alkali metal cation increases. No activated dissociation was observed for alkali metal cation binding to TMP. The binding of alkali metal cations to TMP is compared with that to acetone and methanol.     

Potassium cation affinities of matrix assisted laser desorption ionization matrices determined by threshold collision-induced dissociation: application to benzoic acid derivatives

Threshold collision-induced dissociation of K+(xBA) complexes with xenon is studied using guided ion beam mass spectrometry. The xBA ligands studied include benzoic acid and all of the mono- and dihydroxy-substituted benzoic acids: 2-, 3-, and 4-hydroxybenzoic acid and 2,3-, 2,4-, 2,5-, 2,6-, 3,4-, and 3,5-dihydroxybenzoic acid. In all cases, the primary product corresponds to endothermic loss of the intact xBA ligand. The cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for K+-xBA after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of the xBA ligands and their complexes with K+. Theoretical BDEs are determined from single-point energy calculations at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels using B3LYP/6-31G* optimized geometries. Four favorable binding modes for the K+(xBA) complexes are found. In all complexes to an xBA ligand that does not have a 2-hydroxyl substituent, the most favorable binding mode corresponds to a single interaction with the carbonyl oxygen atom. Formation of a 4-membered ring via chelation interactions with both oxygen atoms of the carboxylic acid group is found to be the most favorable binding mode for all of the 2-hydroxy-substituted systems except K+(2,3-dihydroxybenzoic acid). In these complexes, a hydrogen-bonding interaction between the hydrogen atom of the carboxylic acid moiety and the oxygen atom of the 2-hydroxy substituent provides additional stabilization. Formation of a 5-membered chelation ring via interaction of K+ with the oxygen atoms of adjacent hydroxyl substituents is also favorable and corresponds to the ground-state geometry for the K+(23DHBA) complex. Formation of a 6-membered chelation ring via interaction of K+ with the carbonyl and 2-hydroxyl oxygen atoms is also quite favorable but does not correspond to the ground-state geometry for any of the systems examined here. The experimental BDEs determined here are in very good agreement with the calculated values.     

Dipole effects on cation-pi interactions: absolute bond dissociation energies of complexes of alkali metal cations to N-methylaniline and N,N-dimethylaniline

Threshold collision-induced dissociation of M (+)( nMA) x with Xe is studied using guided ion beam mass spectrometry, where nMA = N-methylaniline and N, N-dimethylaniline and x = 1 and 2. M (+) includes the following alkali metal cations: Li (+), Na (+), K (+), Rb (+), and Cs (+). In all cases, the primary dissociation pathway corresponds to the endothermic loss of an intact nMA ligand. The primary cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for ( nMA) x-1 M (+)-( nMA) after accounting for the effects of multiple ion-neutral collisions, the internal and kinetic energy distributions of the reactants, and the dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes, which are also used in single-point calculations at the MP2(full)/6-311+G(2d,2p) level to determine theoretical BDEs. The results of these studies are compared to previous studies of the analogous M (+)(aniline) x complexes to examine the effects of methylation of the amino group on the binding interactions. Comparisons are also made to a wide variety of cation-pi complexes previously studied to elucidate the contributions that ion-dipole, ion-induced-dipole, and ion-quadrupole interactions make to the overall binding.     

Sodium cation affinities of MALDI matrices determined by guided ion beam tandem mass spectrometry: application to benzoic acid derivatives

Threshold collision-induced dissociation of Na(+)(xBA) complexes with Xe is studied using guided ion beam mass spectrometry. The xBA ligands studied include benzoic acid and all of the mono- and dihydroxy-substituted benzoic acids: 2-, 3-, and 4-hydroxybenzoic acid and 2,3-, 2,4-, 2,5-, 2,6-, 3,4-, and 3,5-dihydroxybenzoic acid. In all cases, the primary product corresponds to endothermic loss of the intact xBA ligand. The cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for Na(+)-xBA after accounting for the effects of multiple ion-neutral collisions, internal and kinetic energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes and provide the molecular constants necessary for the thermodynamic analysis of the experimental data. Theoretical BDEs are determined at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels using the B3LYP/6-31G* optimized geometries. The trends in the measured BDEs suggest two very different binding modes for the Na(+)(xBA) complexes, while theory finds four. In general, the most stable binding conformation involves the formation of a six-membered chelation ring via interaction with the carbonyl and 2-hydroxyl oxygen atoms. The ground state geometries of the Na(+)(xBA) complexes in which the ligand does not possess a 2-hydroxyl group generally involve binding of Na(+) to either the carbonyl oxygen atom or to both oxygen atoms of the carboxylic acid group. These binding modes tend to be competitive because the enhancement in binding associated with the chelation interactions in the latter is mediated by steric repulsion between the hydroxyl and ortho hydrogen atoms. When possible, hydrogen bonding interactions with the ring hydroxyl group(s) enhance the stability of these complexes. The agreement between the theoretical and experimental BDEs is quite good for B3LYP and somewhat less satisfactory for MP2(full).     

Sodium Cation Affinities of Commonly Used MALDI Matrices Determined by Guided Ion Beam Tandem Mass Spectrometry

The sodium cation affinities of six commonly used MALDI matrices are determined here using guided ion beam tandem mass spectrometry techniques. The collision-induced dissociation behavior of six sodium cationized MALDI matrices, Na⁺(MALDI), with Xe is studied as a function of kinetic energy. The MALDI matrices examined here include: nicotinic acid, quinoline, 3-aminoquinoline, 4-nitroaniline, picolinic acid, and 3-hydroxypicolinic acid. In all cases, the primary dissociation pathway corresponds to endothermic loss of the intact MALDI matrix. The cross section thresholds are interpreted to yield zero and 298 K Na⁺−MALDI bond dissociation energies (BDEs), or sodium cation affinities, after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* and MP2(full)/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory are used to characterized the structures and energetics for these systems. The calculated BDEs exhibit very good agreement with the measured values for most systems. The experimental and theoretical Na⁺−MALDI BDEs determined here are compared with those previously measured by cation transfer equilibrium methods.     

Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.     

Modeling metal cation-phosphate interactions in nucleic acids in the gas phase via alkali metal cation-triethyl phosphate complexes

Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations, Na+, K+, Rb+, and Cs+, to triethyl phosphate (TEP). The primary and lowest energy dissociation pathway in all cases is the endothermic loss of the neutral TEP ligand. Theoretical electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31G* level of theory are used to determine the structures, molecular parameters, and theoretical estimates for the BDEs of these complexes. For the complexes to Rb+ and Cs+, theoretical calculations were performed using hybrid basis sets in which the effective core potentials and valence basis sets of Hay and Wadt were used to describe the alkali metal cation, while the standard basis sets were used for all other atoms. The agreement between theory and experiment is excellent for the complexes to Na+ and K+ and is somewhat less satisfactory for the complexes to the heavier alkali metal cations, Rb+ and Cs+, where effective core potentials were used to describe the cation. The trends in the binding energies are examined. The binding of alkali metal cations to triethyl phosphate is compared with that to trimethylphosphate.     

Tautomerization in the formation and collision-induced dissociation of alkali metal cation-cytosine complexes

Noncovalent interactions between alkali metal cations and the various low-energy tautomeric forms of cytosine are investigated both experimentally and theoretically. Threshold collision-induced dissociation (CID) of M(+)(cytosine) complexes with Xe is studied using guided ion beam tandem mass spectrometry, where M(+) = Li(+), Na(+), and K(+). In all cases, the only dissociation pathway observed corresponds to endothermic loss of the intact cytosine molecule. The cross-section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for the M(+)(cytosine) complexes after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Ab initio calculations are performed at the MP2(full)/6-31G* level of theory to determine the structures of the neutral cytosine tautomers, the M(+)(cytosine) complexes, and the TSs for unimolecular tautomerization. The molecular parameters derived from these structures are employed for the calculation of the unimolecular rates for tautomerization and the thermochemical analysis of the experimental data. Theoretical BDEs of the various M(+)(cytosine) complexes and the energy barriers for the unimolecular tautomerization of these complexes are determined at MP2(full)/6-311+G(2d,2p) level of theory using the MP2(full)/6-31G* optimized geometries. In addition, BDEs for the Li(+)(cytosine) complexes are also determined at the G3 level of theory. Based upon the tautomeric mixture generated upon thermal vaporization of cytosine, calculated M(+)-cytosine BDEs and barriers to tautomerization for the low-energy tautomeric forms of M(+)(cytosine), and measured thresholds for CID of M(+)(cytosine) complexes, we conclude that tautomerization occurs during both complex formation and CID.     

The special five-membered ring of proline: An experimental and theoretical investigation of alkali metal cation interactions with proline and its four- and six-membered ring analogues

The interaction of the alkali metal cations, Li+, Na+, and K+, with the amino acid proline (Pro) and its four- and six-membered ring analogues, azetidine-2-carboxylic acid (Aze) and pipecolic acid (Pip), are examined in detail. Experimentally, threshold collision-induced dissociation of the M+(L) complexes, where M = Li, Na, and K and L = Pro, Aze, and Pip, with Xe are studied using a guided ion beam tandem mass spectrometer. From analysis of the kinetic energy dependent cross sections, M(+)-L bond dissociation energies are measured. These analyses account for unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. Ab initio calculations for a number of geometric conformations of the M+(L) complexes were determined at the B3LYP/6-311G(d,p) level with single-point energies calculated at MP2(full), B3LYP, and B3P86 levels using a 6-311+G(2d,2p) basis set. Theoretical bond energies show good agreement with the experimental bond energies, which establishes that the zwitterionic form of the alkali metal cation/amino acid, the lowest energy conformation, is formed in all cases. Despite the increased conformational mobility in the Pip systems, the Li+, Na+, and K+ complexes of Pro show higher binding energies. A meticulous examination of the zwitterionic structures of these complexes provides an explanation for the stability of the five-membered ring complexes.     

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^*)。     

A theoretical investigation on the structures,densities, detonation properties,and pyrolysis mechanism of the nitro derivatives of phenols

The nitro derivatives of phenols are optimized to obtain their molecular geometries and electronic structures at the DFT‐B3LYP/6‐31G* level. Detonation properties are evaluated using the modified Kamlet–Jacobs equations based on the calculated densities and heats of formation. It is found that there are good linear relationships between density, detonation velocity, detonation pressure, and the number of nitro and hydroxy groups. Thermal stability and pyrolysis mechanism of the title compounds are investigated by calculating the bond dissociation energies (BDEs) at the unrestricted B3LYP/6‐31G* level. The activation energies of H‐transfer reaction is smaller than the BDEs of all bonds and this illustrates that the pyrolysis of the title compounds may be started from breaking O? H bond followed by the isomerization reaction of H transfer. Moreover, the C? NO₂ bond with the smaller bond overlap population and the smaller BDE will also overlap may be before homolysis. According to the quantitative standard of energetics and stability as a high‐energy density compound, pentanitrophenol essentially satisfies this requirement. In addition, we have discussed the effect of the nitro and hydroxy groups on the static electronic structural parameters and the kinetic parameter. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Computational DFT studies on a series of toluene derivatives as potential high energy density compounds

Based on the full optimized molecular geometric structures at B3LYP/6-31G**, B3LYP/6-31+G**, B3P86/6-31G**, and B3P86/6-31+G** levels, the densities (ρ), detonation velocities (D), and pressures (P) for a series of toluene derivatives, as well as their thermal stabilities, were investigated to look for high energy density compounds (HEDCs). The heats of formation (HOFs) are also calculated via designed isodesmic reactions. The calculations on the bond dissociation energies (BDEs) indicate that the BDEs of the initial scission step are between 48 and 59 kcal/mol, and pentanitrotoluene is the most reactive compound, while 2,4,6-trinitrotoluene is the least reactive compound for toluene derivatives studied. A good linear relationship between BDE/E and impact sensitivity is also obtained. The condensed phase HOFs are calculated for the title compounds. These results would provide basic information for the further studies of HEDCs. The detonation data of pentanitrotoluene show that it meets the requirement for HEDCs.     

Cation-pi interactions: structures and energetics of complexation of Na+ and K+ with the aromatic amino acids, phenylalanine, tyrosine, and tryptophan

Threshold collision-induced dissociation of M(+)(AAA) with Xe is studied using guided ion beam tandem mass spectrometry. M(+) include the alkali metal ions Na(+) and K(+). The three aromatic amino acids are examined, AAA = phenylalanine, tyrosine, or tryptophan. In all cases, endothermic loss of the intact aromatic amino acid is the dominant reaction pathway. The threshold regions of the cross sections are interpreted to extract 0 and 298 K bond dissociation energies for the M(+)-AAA complexes after accounting for the effects of multiple ion-neutral collisions, internal energy of the reactant ions, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures of the neutral aromatic amino acids and their complexes to Na(+) and K(+) and to provide molecular constants required for the thermochemical analysis of the experimental data. Theoretical bond dissociation energies are determined from single-point energy calculations at the B3LYP/6-311++G(3df,3pd) level using the B3LYP/6-31G geometries. Good agreement between theory and experiment is found for all systems. The present results are compared to earlier studies of these systems performed via kinetic and equilibrium methods. The present results are also compared to the analogous Na(+) and K(+) complexes to glycine, benzene, phenol, and indole to elucidate the relative contributions that each of the functional components of these aromatic amino acids make to the overall binding in these complexes.     

Structural and Energetic Effects in the Molecular Recognition of Acetylated Amino Acids by 18-Crown-6

Absolute 18-crown-6 (18C6) binding affinities of four protonated acetylated amino acids (AcAAs) are determined using guided ion beam tandem mass spectrometry techniques. The AcAAs examined in this work include: N-terminal acetylated lysine (N_???CAcLys), histidine (N_???CAcHis), and arginine (N_???CAcArg) as well as side chain acetylated lysine (N_???CAcLys). The kinetic-energy-dependent cross sections for collision-induced dissociation (CID) of the (AcAA)H⁺(18C6) complexes are analyzed using an empirical threshold law to extract absolute 0 and 298?K (AcAA)H⁺?18C6 bond dissociation energies (BDEs) after accounting for the effects of multiple collisions, kinetic and internal energy distributions of the reactants, and unimolecular dissociation lifetimes. Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the AcAAs as well as the proton bound complexes of these species, (AcAA)H⁺(18C6), at the B3LYP/6-311+G(2d,2p)//B3LYP/6-31?G* and M06/6-311+G(2d,2p)//B3LYP/6-31G* levels of theory. For all four (AcAA)H⁺(18C6) complexes, loss of neutral 18C6 corresponds to the most favorable dissociation pathway. At elevated energies, products arising from sequential dissociation of the primary CID product, H⁺(AcAA), are also observed. Protonated N_???CAcLys exhibits a greater 18C6 binding affinity than other protonated N_???CAcAAs, suggesting that the side chains of Lys residues are the preferred binding sites for 18C6 complexation to peptides and proteins. N_???CAcLys exhibits a greater 18C6 binding affinity than N_???CAcLys, suggesting that binding of 18C6 to the side chain of Lys residues is more favorable than to the N-terminal amino group of Lys.     

Molecular Structure of Complexes with Bifurcated Hydrogen Bond: I. N-(4-Methyl-2-nitrophenyl)acetamide

According to the results of HF/6-31G* and B3LYP/6-31G* nonempirical calculations, N-(4-methyl- 2-nitrophenyl)acetamide in the synperiplanar and antiperiplanar conformations gives stable complexes with protophilic solvents, which are stabilized by bifurcated (three-center) hydrogen bond. The complexes are characterized by (1) opposite variations of the interatomic distances and angles corresponding to intra- and intermolecular components of the bifurcated hydrogen bond, (2) extension of the intramolecular component and a more pronounced shortening of the intermolecular component with increase in the strength of the three-center H-complex, and (3) nonlinear and nonmonotonic relation between the NH stretching vibration frequency and the energy of complex formation.     

Conformational study of the structure of 12-crown-4-alkali metal cation complexes

A conformational search was performed for the 12-crown-4 (12c4)-alkali metal cation complexes using two different methods, one of them is the CONFLEX method, whereby eight conformations were predicted. Computations were performed for the eight predicted conformations at the HF/6-31+G*, MP2/6-31+G*//HF/6-31+G*, B3LYP/6-31+G*, MP2/6-31+G*//B3LYP/6-31+G*, and MP2/6-31+G* levels. The calculated energies predict a C4 conformation for the 12c4-Na+, -K+, -Rb+, and -Cs+ complexes and a C(s) conformation for the 12c4-Li+ complex to be the lowest energy conformations. For most of the conformations considered, the relative energies, with respect to the C4 conformation, at the MP2/6-31+G*//B3LYP/6-31+G* are overestimated, compared to those at the MP2/6-31+G* level, the highest level of theory considerd in this report, by 0.2 kcal/mol. Larger relative energy differences are attributed to larger differences between the B3LYP and MP2 optimized geomtries. Binding enthalpies (BEs) were calculated at the above-mentioned levels for the eight conformations. The agreement between the calculated and experimental BEs is discussed.     

Understanding selenocysteine through conformational analysis,proton affinities,acidities and bond dissociation energies

Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6‐31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6‐311++G*//B3LYP/6‐31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008