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The full catalytic mechanism for nitrile hydratase is explored, involving cysteine-sulfenic acid acting as a nucleophile, activating a water molecule to attack nitrile substrates. The iminol intermediate undergoes tautomerization to form the amide product. The computed enthalpies are closely related to experimental values, suggesting the current mechanism with two water molecules should be further investigated.

To prepare for future resistance, new methods are being explored for novel treatment of malaria. The current work uses high performance docking methods to model different substrates binding into the active sites of varying Homo sapien and Plasmodium peptidyl-prolyl cis/trans isomerase enzymes and compares their subsequent docking scores. This approach has shown that the substrates ILS-920 and WYE-592 will bind less-favourably with hFKBP12 and PfFKBP35 compared to a competing substrate rapamycin; however, the binding appears to be more favourable in PvFKBP35. This could suggest a possible target for inhibition of the Plasmodium vivax parasite.

The local and regional stabilities in clusters of water, methanol, and formaldehyde up to the tetramers have been analyzed from an atomic energy perspective. We optimize structures at the MP2/6-311++G(d,p) level with some CCSD(T)/6-311++G(d,p) single point energies, and then decompose the electronic densities into atomic parts using the atoms in molecules (AIM) approach. We consider the changes in atomic energy in the clusters vs. the isolated monomer. This method of analysis allows us to reveal the variety of stabilities within these hydrogen-bonded clusters, including indications of cooperative, anti-cooperative, and non-cooperative interactions. Cooperatively interacting clusters have increasing stability at the atomic level as the cluster size grows. This is not observed in the anti- and non-cooperative arrangements of water and formaldehyde clusters. The cooperativity in methanol clusters is dominated by the OH regions, with negligible energy change in the methyl regions. Formaldehyde clusters, including the lowest minimum “bucket” cluster, do not show significant cooperativity. Atomic energy analysis is supported with bond critical point data as well as charge and geometric values. We represent the local stability in the clusters using a simple visual approach that allows areas of increased or decreased stability to be easily interpreted.

Organotin compounds are very important in material design as well as in biomedical and biochemical applications. However, little is known about their BDEs experimentally or computationally. Thus, a variety of common quantum chemical methods in combination with several approaches to treating relativistic effects of the tin core electrons were used to calculate the BDEs of organotin compounds. Our results show that the BDEs are very sensitive to the choice of the computational method and to the treatment of relativistic effects.

α-Helical peptides of the form For-AAAAAAXAAAAAA-NH 2 , where X is one of 21 amino acids, have been optimized by use of density-functional theory with the inclusion of solvent by a polarizable continuum model and analyzed by use of the quantum theory of atoms in molecules. Inclusion of solvent results in the transition from a partial 3 10 -helix geometry that was previously observed in gas-phase optimized structures to a fully α-helical geometry, resulting in a substantial loss of NH⋯O i + 3 contacts and concurrent formation of NH⋯O i + 4 contacts. An increase in the number of N⋯O i + 3 contacts was also observed. The total electron density (∑ ρ ( r c )) at the hydrogen bond critical points (HBCPs) within the peptide backbone increased by up to 160% in the solvated structure. No correlation was found between the ∑ ρ ( r c ) at HBCPs and an α-helix propensity scale, however, the ∑ ρ ( r c ) at HBCPs for the substituted amino acids yields a helix-stabilizing order for the amino acids: Thr > Asn > Ser > Glu > Trp > Arg > Asp > Leu > Cys > His + >Gln > Lys > Met > Ile > Val > Phe > His > Ala > Tyr > Pro > Gly.

Analogues of the antioxidant ethoxyquin are studied to determine the effects of changing the group 16 element in the reacting center of a glutathione peroxidase mimic. The energy barrier for hydrogen peroxide reduction decreases along the group, with sulfur showing the highest, selenium intermediate, and tellurium the lowest barrier. The ethyl side chain on the chalcogen is substituted with methyl and tertiary-butyl groups to determine the degree of steric effects on the barrier. A phenyl substituent results in a higher barrier than the alkyl side chains.

Inspired by the helical structure as well as the conductivity of DNA and substituted polyphenylacetylenes, a new kind of substituted polyacetylene is introduced. More specifically, polycytosineacetylene ((RC CH) n , R = cytosine) with a trans-polyacetylene backbone is investigated theoretically. The neutral and cationic geometries are optimized as single helical chains with n = 20. It is found that when an electron is removed the polymer stretches from 19.80 A to 28.41 A. The polyacetylene backbone in the optimized cationic polymer exhibits the formation of a soliton. It is predicted that a doped polycytosineacetylene would have good conductivity, and would also behave as a nanomechanical spring and as a piezoelectric material.

We propose a general definition of the radius of an atom in terms of its ionization energy. A relationship between these two fundamental properties is derived from the radial distribution function and the exponential decay of the electron density. Strong correlations with well-known atomic radii lead us to conclude that we have found a universally valid definition of the atomic radius, defined exclusively in terms of an intrinsic property, the ionization energy of an atom, which is equally available from experiments and theoretical computations.

Triply hydrogen-bonded complexes of the form AAA-DDD are shown to have the strongest interaction when the complex is substituted with electron withdrawing groups on the donor molecule (DDD) and electron donating groups on the acceptor molecule (AAA). In particular, the largest effects are observed when the withdrawing groups act through resonance. This serves to flatten the entire system resulting in more linear, and consequently stronger, hydrogen bonds. Furthermore, the present calculations show that the binding energy correlates with the electron density at the bond critical points and inversely with the hydrogen bond lengths.

The Paal–Knorr pyrrole synthesis, which involves the reaction of 1,4-dicarbonyls with amines, is among the most classical methods of heterocyclic pyrrole ring synthesis. The detailed sequence and the nature of the intermediates that occur in the Paal–Knorr reaction mechanism are not well understood. Density functional theory methods have been employed to investigate the nature of the intermediates and transition states in the Paal–Knorr pyrrole mechanism. Two mechanistic pathways for the reaction were examined: hemiaminal cyclization vs. enamine cyclization. Our calculated reaction potential energy surfaces suggest that the hemiaminal cyclization is the preferred pathway for the reaction both in gas phase and in solution. This conclusion is consistent with the experimental results which suggest that the hemiaminal intermediate undergoes cyclization in the rate-limiting step in the Paal–Knorr reaction mechanism. The preferred mechanism for the Paal–Knorr reaction consists of hemiaminal formation, hemiaminal cyclization and a dehydration step to form the pyrrole ring. Water and hydrogen-bonding interactions play a key role in catalyzing the hydrogen-transfer steps of the reaction.

We report a study of the inclusion complex of p-chlorophenol inside α-cyclodextrin (α-CD) by the theory of atoms in molecules (AIM). We use a quantitative comparison of some AIM properties of isolated p-chlorophenol (PCP) and the inclusion complex (PCP-CD) and we characterize some weak interactions within the host–guest complex. Furthermore, we compare the electrophilic aromatic substitution on the p-chlorophenol in the isolated state and inside α-CD. The analysis of the bond critical points of PCP shows that there is no trend in the effect on the AIM properties of PCP due to inclusion in the α-CD.

A type of cage critical point (CCP) that has remained so far only a ‘mathematical possibility’ is reported for the first time. A CCP enclosed by two ring surfaces is found in a single ring in each of three derivatives of 1,12-difluorobenzo[c]phenanthrene. The two fluorine nuclei are linked by a bond path which results in the closure of a seven-membered ring in the ‘bay’ region. The crowding of the fluorine atoms forces an α-helical (staircase) twisting of the molecule causing the ring surface to split into two giving rise to a CCP. The Poincare–Hopf relationship is satisfied in each case.

We report a detailed characterization of the valence shell charge concentration (VSCC) of fluorine in methyl fluoride through the atoms in molecules theory. A comparison between the VSCCs of fluorine and neighboring elements (N, O, P, S, Cl) in the periodic table is also presented. The fluorine VSCC is shown to be tetrahedral and the most compact with the highest values of ρ and −∇ 2 ρ . Our results calculated at several post Hartree–Fock levels of theory using a large basis set show a remarkable insensitivity to the level of theory.

The performance of the DFT functionals B3LYP, B3PW91 and PBE1PBE in conjunction with selected basis sets for the prediction of 15N and 13C nuclear shieldings for small nitrogen-containing molecules is assessed. For molecules containing only singly bonded nitrogen and carbon atoms, the PBE1PBE/6-311+G(2df,p) level of theory is shown to provide reliable 15N and 13C nuclear shieldings. For the triply bonded nitrogen-containing molecules N2, CH3CN and HCN, all three levels of theory are much less satisfactory.

The gas phase and solution electron affinities and ionization potentials of uracil, thymine and a series of 5-halouracils ( 5XU, X=F, Cl, Br ) are investigated with B3LYP. Halogen substitution has a smaller effect on the IP than the EA of U . The EAs are calculated to increase according to T U 5FU 5ClU 5BrU . The calculated barriers for the dissociation of the resulting 5XU anions to X − plus uracil-centered radicals decrease along the series 5FU − > 5ClU − > 5BrU − . The calculated trends are consistent with suggestions that 5XUs enhance the sensitivity of deoxyribonucleic acid, DNA (ribonucleic acid, RNA) to ionizing radiation and that 5BrU leads to the greatest enhancement.

We have derived the conditions that an exact non-relativistic molecular wavefunction must fulfill at two critical points, namely, at the nucleus–electron cusp (when the position of an electron is coincident with a nucleus) and the electron–electron cusp (when the position of two arbitrary electrons coincide at a point). The interaction potential between the electrons and nuclei has not been restricted to the Coulombic form, but given a general distance dependent form. Using the derived cusp conditions for the wavefunction we have obtained the conditions that rule the one-electron density and the intracule density for the nucleus–electron and the electron–electron cusps, respectively. Finally, the results obtained for the harmonic, Yukawa and Hulthen potentials are illustrated.

Density-functional theory (B3LYP functional) is used to investigate the ionization potentials and electron affinities of the DNA and RNA nucleotide bases. For the first time, anions lying lower in energy than the neutral species have been calculated for both thymine and uracil (i.e., positive adiabatic electron affinities). Additionally, the calculations show that anion formation leads to significant geometrical changes to the nucleobases. This is a very important finding as previous calculations have indicated that the anions are very similar in geometry to the neutral species and reported negative valence adiabatic electron affinities.

The molecular quadrupole moments of benzene and naphthalene are calculated using a range of ab initio and density functional methods, with basis sets as large as aug-CC-PVTZ for benzene and CC-PVTZ for naphthalene. The quadrupole moments calculated using Hartree-Fock wavefunctions are lower than the experimentally determined values, and all DFT values are higher than the experimental values. The use of the hybrid B3P86 and B3PW91 functionals, with a large basis set, produce quadrupole moments which are within experimental error for these two small aromatic molecules.

The structures and relative stabilities of the four different forms of hydroxypyridine and hydroxyquinoline (normal, protonated cation, deprotonated anion and zwitterion) in the gas phase have been calculated at the Moller-Plesset (MP) perturbation and coupled-cluster theory levels with basis sets up to 6–31+ G ∗∗ . The solvation free energies of the reactions were treated with the SMx series of aqueous solvation models by Cramer and Truhlar. By combining the PM3-SM3 model for solvation with the MP 2/6–31+ G ∗∗ level treatment for the gass-phase species, it is found that the free energy changes of the proton transfer reactions can be predicted reasonably well.

The thermally induced decomposition of ethylene, C2H4, to acetylene, C2H2, on the Ni(111) surface has been treated theoretically: potential-energy curves were computed within a modified extended-Huckel framework and reaction rates estimated via a master equation approach. As a preliminary step, adsorbate geometries and binding energies were optimized for one and two molecules of each hydrocarbon species chemisorbed in various sites on rigid bulk cluster models of the Ni substrate. A fragmentation pathway is proposed, eliciting the concerted tunnelling of intermolecular H's from a transient bimolecular complex comprised of two rotated C2H4's, which rationalizes the observed second-order decomposition kinetics.

The internal motion of benzene is studied in the gas phase at 30 and 300 K and in the liquid phase at 300 K by means of a molecular dynamics method based on a hybrid of quantum and molecular mechanical force fields. The fluctuations of bond lengths, bond angles and torsional angles are calculated and compared with available experimental data. A conformational analysis for the planar, boat, chair and twisted structures of benzene is carried out and liquid benzene is found to be effectively a planar hexagon at room temperature.

The interactions between an alkali metal atom (Li, Na, K) and acetylene/vinylidene are investigated by means of gradient corrected (‘PWP’) density functional theory. Particular emphasis is made on the determination of equilibrium geometries, energetics and atomic hyperfine structures of the MHCCH van der Waals addition complexes, and the MHCCH and MCCH2 charge-transfer complexes. The PWP optimized geometries are found to be similar to previous ab initio data, and the generated hyperfine structures are in excellent accord with experimental matrix isolation ESR data recorded at 4 K. In the charge transfer complex formation, the metal atoms are found to donate 0.6–0.8 electron from an excited p orbital to the antibonding CC π∗ orbital of the hydrocarbon fragment. The calculated trend in charge donation matches the order of increasing atomic s → p excitation energies, K < Li < Na. This is the first application of the present method to metal atom hyperfine structures, and the results are promising for future studies.

Density functional theory calculations of isotropic couplings of the atoms B to O are carried out with a variety of functional forms and basis sets. It is shown that the atomic isotropic coupling constants are very dependent on functional form, auxiliary basis set and orbital set. The calculations on the molecular systems NH 2 and H + 3 show less dependence for isotropic couplings and almost independence for anisotropic couplings. It is found that the combination of Perdew and Wang's non-local exchange functional and Perdew's correlation correction functional with a [7s, 6p, 2d]/(5, 2; 5, 2) orbital/auxiliary basis set gives results in semiquantitative agreement with experiment and MRSDCI calculations.

The influence of up to six Ne atoms on the isotropic hyperfine (hf) coupling constants of the hydrogen atoms in CH+4 is investigated using density functional theory. It is found that at very short NeH distances (R = 1.8 A), the hf structure is strongly affected, whereas at the more realistic van der Waals distance (R ≈ 2.5 A), the methane radical experiences a very weak field from the surrounding Ne atoms. At larger distances, the effects of the Ne matrix are negligible. It is furthermore found that at small R, the changes in aiso (H) are strongly dependent on the relative positions of the Ne atoms.

Multireference configuration interaction calculations for the low-lying electronic states of C2 (a 3Πu and A 1Πu) and O2 (X 3Σg−, a 1Δg) over a range of internuclear separations reveal that the singlet-triplet electron-electron repulsion energy differences tend to have the same sign as the singlet-triplet kinetic energy differences, while the corresponding electron-nuclear attraction energy differences tend to have the opposite sign at a given geometry. Adiabatic energy component differences for C2 and O2 show that the electron-electron repulsion in the triplet state is greater than in the singlet state, while there is more electron-nuclear attraction in the triplet than in the singlet state. The latter observations are consistent with the results for atomic states arising from the same configuration, but are contrary to the traditional explanation of Hund's rule.

Ab initio SCF MO calculations for the hydrogen-bonded complexes between nitriles and hydrogen fluoride suggest a strong linear relationship between the charge density at the hydrogen-bond critical point and the hydrogen-bond energy. Further investigation of the topological properties of the charge density indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader et al. may be extended to intermolecular hydrogen bonding. Calculations at the 6–31G ** level, including complete geometry optimization, are reported for the complexes, where R  H, Li, F, Cl, HO, LiO, NC, HCC, CH 3 and CH 3 O.

The density difference ΔD(r1), defined as the difference between the exact and the Hartree-Fock radial density functions is reported for the 2 3S and the 2 1S excited states of the helium atom. The density differences in both cases resemble the inverse of the helium ground-state density difference, but are more long-ranged due to the diffuseness of the excited states. The effect of electron correlation on one-electron distributions is also demonstrated by comparison of (r1n) expectation values and several indices of the relative sizes of atoms. Electron correlation leads to a contraction of the Hartree-Fock electron clouds.

The topological properties of the charge density of the hydrogen-bonded complexes between nitrites and hydrogen chloride correlate linearly with theoretical estimates of the hydrogen-bond energy. At the 6-31G** level, the hydrogenbond energies range from a low of 10 kJ mol m NCCN—HC1 to a high of 38 kJ mol in LiCN—HCl. A linear relationship between the charge density at the hydrogen-bond critical point and the NH internuclear distance of the RCN—HC1 complexes indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader, Tang, Tal and Biegler-Konig can be extended to intermolecular hydrogen bonding.

Ab initio SCF MO calculations are reported for benzene, s -triazine, borazine and boroxine. The Laplacian of the charge density and the Mulliken population analysis procedure demonstrate that the delocalization of the π electrons decreases and the polarity of the ring bonds increases substantially as the atoms in the ring become more dissimilar. Several other properties, including distortion of the ring angles, puckering of the ring and nuclear quadrupolar coupling constants, emphasize the different chemical properties within the isoelectronic series.

The effect of water-anion and water-cation interactions on the stretching and bending force constants of a water molecule was studied by ab initio calculations. The OH stretching force constant f, is decreased by water-anion and water-cation interactions, its decrease correlating linearly with the elongation of the O-H bond length. The H-O-H bending force constantj= is increased by anion attachment but appears to be almost unaffected by cation attachment. The observed near-constancy off, upon cation attachment is internreted as the result of a decrease due to C%H bond elongation and an approximately equal increase due to greater forces opposing the bending motion. and F- . HOH . F- (VI), which were optimized under C,, symmetry. The optimized geometries of V and VI correspond to potential minima only under the constraint of C,, symmetry; the two complexes are unstable with respect to dissociation into a free ion and an ion-molecule complex. METHOD OF CALCULATION

Potential curves for the ground and all excited singlet states which dissociate into the ground states of the atoms, Cl(2pu) and F(2Pu), or into the ionic species, Cl+(1Dg) and F−(1Sg), have been calculated by means of the multi-reference configu interaction (MRD CI) method. The Gaussian basis set consists of a total of 70 contracted functions, including Rydberg and bond functions. The calculations show that adequate treatment of Rydberg-valence mixing is essential for an understanding of the ClF electronic absorption spectrum. The calculated Do value for the ground state is 2.47 eV compared to the experimental value of 2.617 eV. Transitions of potential spectroscopic interest include the dipole allowed 1Σ+ → 1/gP transition, having a vertical transitio energy of 8.92 eV, and the allowed 1Σ+ → 1Σ+ transition, with a vertical transition energy of 10.3 eV.

Density difference functions, defined in terms of the radial density function of an ion and the corresponding neutral atom, reveal the changes in the charge cloud which occur when an electron is removed from an alkali metal atom or added to a halogen atom. The changes are not restricted to the valence region. Removal of an electron from a Group IA element leads to a reduction of the valence-shell electron density, whereas adding an electron to a halogen increases the electron density in the valence region. For both types of ions, substantial increases and decreases in the electron density are observed in the inner shells. Explicit calculations are presented for the Li+, Na+, K+, Rb+, F−, Cl−, Br− and I− ions at the Hartree-Fock level.

Single determinant ab initio molecular orbital theory has been applied to the description of the equilibrium geometries, total energies, atomization energies, force constants, dipole moments and total atomic charges of the first five cyanopolyynes, H(CC) n CN. Hydrogen cyanide and acetylene are included for comparison. In order to study the basis set dependence of the computed properties, three methods of introducing more flexibility into the STO-3G minimal basis set have been considered: increasing the number of primitives, introducing split-valence basis sets and adding polarization functi The mean absolute deviation between the theoretical and observed bond lengths decreases along the series STO-3G, STO-6G, 3-21G, 4-31G and 6-31G. The relatively new 3-21G split-valence basis set leads to the best agreement with the experimental dipole moments. At the STO-NG level the net atomic charg and equilibrium bond lengths are observed to tend monotonically, as a function of chain length, to certain asymptotic values. Due to cancellation of errors in the CC and CC bond lengths, the STO-3G basis set yields estimates of the rotational constant, B e , for the larger cyano which are expected to be too large by about 0.6%.

Electronic population changes and the evolution of the contour maps of the charge density and its Laplacian are used to study the polarizability of hydrogen bonds as a function of the position of the proton within the hydrogen bond. Standard ab initio molecular orbital theory at the 4–31G level (44-31G* for sulphur) has been used to study the complexes between the acceptors, formaldehyde and thioformaldehyde, and the donors, hydrogen fluoride and the ammonium cation. A number of important conclusions for the interpretation of infrared spectra are discussed.

Hartree—Fock wavefunctions and good approximations to the exact wavefunctions are used to demonstrate the effect of electron correlation on the radial density D ( r 1 ) and the contours of the density distribution ϱ( r 1 ) in the He isoelectronic sequence. In general, correlation effects diminish as the charge-cloud becomes less diffuse.

The orbital energies and charge densities in borazine were calculated by the Huckel M.O. method. the Bond Electronegativity Equalization Method for σ and π electrons (BEEM-π) and by the Semi-Emperical All Vallence electron theory with complete neglect of differential overlap (SAVE-CNDO).