Abstract

Theoretical justication for preferential heterochiral cyclic trimerization of 5- (aminoethyl)-2-furancarboxylic acid (AEFC) is attempted using density functional theory (DFT) calculations. Results from explicit solvent assisted reaction pathways indicate greater stability of heterochiral cyclic tripeptides over their homochiral counterparts, contrary to ndings from gas phase and implicit solvent phase results. Pathways explored at M06/6- 31G(d,p) and MP2/6-31G(d,p) levels of theory show kinetic preference for heterochiral cy- clization. Analysis of optimized geometries reveals existence of strong hydrogen bonding interactions in the solvated heterochiral tripeptides. Thus, the ability of the cyclic tripep- tides to form strong noncovalent interactions increases with conversion of stereochemistry at one of its chiral centers from homo to heterochiral conformation. The resulting change in molecular symmetry facilitates the interacting sites to reorient such that the peptide can in- teract with a nucleophile from both the faces. This is further substantiated by computed IR spectra, NBO and AIM data. Additionally, justication for the stability of heterochiral cyclic tripeptides comes from molecular electrostatic potential and electron density surfaces. These studies show clearly that for the kind of systems presented here, gas phase or implicit sol- vent phase studies are inadequate in explaining realistic situations. Calculations with solvent molecules, even if a few only, are necessary to substantiate experimental observations.

Abstract

: Density functional B3LYP method was used to investigate the preference of intra and intermolecular cyclizations of linear tripeptides containing tetrahydrofuran amino acids. Two distinct model pathways were conceived for the cyclization reaction and all possible transition states and intermediates were located. Analysis of the energetics indicate intermolecular cyclization being favored by both thermodynamic and kinetic control. Geometric and NBO analyses were performed to explain the trends obtained along both the reaction pathways. Conceptual density functional theory based reactive indices also show that reaction pathways leading to intermolecular cyclization of the tripeptides are relatively more facile compared to intramolecular cyclization.

Abstract

We have applied genetic algorithm optimization for the design of laser pulses to control dissociation process in the ground electronic state of HF molecule, within the mathematical framework of optimal control theory. In order to design the experimentally feasible laser fields, we coded the small set of selected field parameters in the GA parameter space. Two types of pulses, one with fixed frequency components and the other having non-deterministic components have been designed. Optimized laser field obtained using this approach, possesses simple time and frequency structures. We show that the fields having non-deterministic frequency components lead to greater dissociation probability compared to the ones having deterministic frequency components.

Abstract

Interaction of proline with gold cluster was studied using density functional theory (DFT). Two types of mixed basis sets UB3LYP/6-311++G LANL2MB and UB3LYP/6-311++G LANL2DZ were used for optimization of complex structures. Proline interacts with gold cluster either through one anchor bond, N-Au or an anchor bond O-Au associated with a non-conventional O-H…Au hydrogen bond. Among these interactions, higher tendency for interaction is seen with Au cluster through amide terminal. Natural bond orbital analysis (NBO) is used to substantiate the results.

Abstract

Quantum chemical calculations using density functional theory (DFT) were carried out on systems containing gold atoms attached to amino acids (Proline, Histidine and Arginine). Geometries of amino acids with gold cluster were optimized using the DFT-B3LYP approach. The mixed basis set were used keeping 6-311++G for the amino acid part and 3 dierent basis sets were used for the gold part, i. e., LANL2DZ, LANL2MB and SDD. A comparision of the results using dierent basis sets was made. The interaction between the two moieties has two major components: (a) the anchoring N-Au and O-Au bond and (b) the non covalent interactions between Au and N-H or O-H bonds. The results indicate that there is eective charge transfer from amino acid to the gold cluster. This was conrmed by the natural bond orbital (NBO) analysis. The NBO analysis was also done in order to calculate the charge transfer, natural population analysis (NPA), and Wiberg bond indices of the complexes. The studies also indicated that these bond are partially covalent.

Abstract

Optimal control theory is used to design a laser pulse for the multiphoton dissociation of the Fe– CO bond in the CO-heme compounds. The study uses a hexacoordinated iron–porphyrin– imidazole–CO complex in its ground electronic state as a model for CO liganded to the heme group. The potential energy and dipole moment surfaces for the interaction of the CO ligand with the heme group are calculated using density functional theory. Optimal control theory, combined with a timedependent quantum dynamical treatment of the laser-molecule interaction, is then used to design a laser pulse capable of efficiently dissociating the CO-heme complex model. The genetic algorithm method is used within the mathematical framework of optimal control theory to perform the optimization process. This method provides good control over the parameters of the laser pulse, allowing optimized pulses with simple time and frequency structures to be designed. The dependence of photodissociation yield on the choice of initial vibrational state and of initial laser field parameters is also investigated. The current work uses a reduced dimensionality model in which only the Fe–C and C–O stretching coordinates are explicitly taken into account in the timedependent quantum dynamical calculations. The limitations arising from this are discussed in Sec. IV.

Abstract

Structural and electronic properties of diastereomers of tetrahydrofuran amino acids (TAA) derived tripeptide, Boc-TAA-Leu-Val-OMe, are studied using density functional theory. Predicted secondary folding patterns with hydrogen bonded pseudocycles of different sizes in peptides containing (2R,5S)-cis-TAA and (2S,5R)-cis-TAA are confirmed by detailed NMR studies of both, and single crystal X-ray analysis of the former. A novel unusual folding pattern emanating from three-centered hydrogen bond is found in peptide with (2R,5S)-cis relationship. Stereochemical control on the orientation of interacting sites is substantiated by structural analysis of the peptides. Using natural bonding orbital and atoms in molecules analyses, charge transfer interactions are analyzed.

Abstract

Conventionally optimal control theory has been used in the theoretical design of laser pulses through the direct variation in the electric field of the laser pulse as a function of time. This often leads to designed laser pulses which contain a broad and seemingly arbitrary frequency structure that varies in time in a manner which may be difficult to realize experimentally. In contrast, the experimental design of laser pulses has used a genetic algorithm (GA) approach, varying only those laser parameters actually available to the experimentalist. We investigate in this paper the possibility of using GA optimization methods in the theoretical design of laser pulses to bring about quantum state transitions in molecules. This allows us to select only a small limited number of parameters to vary and to choose these parameters so that they correspond to those available to the experimentalist. In the paper we apply our methods to the vibrational-rotational excitation of the HF molecule. We choose a small limited number of frequencies and vary only the associated electric field amplitudes and pulse envelopes. We show that laser pulses designed in this way can lead to very high transition probabilities.

Abstract

Peptides incorporating 5 membered rings such as furan and tetrahydrofuran (THF) adopt secondary folding patterns and thus mimic natural peptides. The preferred conformation of linear and cyclized peptides incorporating sugar amino acids depends on the stereochemistry of at the chiral center. Control of stereochemistry of THF amino acid (TAA) in the structure of the linear tripeptide Boc-TAA-Leu-Val-OMe containing (2R,5S)-cis TAA, (2S,5R)-cis TAA, (2R,5R)-trans TAA and (2S,5S)-trans TAA is investigated using structural parameters and energetics data obtained from density functional theory (DFT) based calculations at B3LYP/6-31G(d,p) level of theory. We found that the conformations associated with -, - turn structures are stabilized by intramolecular hydrogen bonding interactions. Kinetic control of reactions leading to intra and inter molecular cyclization of tripeptide TAA-Gly-Gly containing (2S,5R)-cis TAA and (2S,5S)-trans TAA is studied at the same level of theory in gas phase[1]. We observe that kinetic control favors cyclodimerization instead of intramolecular cyclization. Theoretical study of reactions leading to linear and cyclic trimerization of backbone altered -peptide, i. e., amino ethyl furan carboxylic acid (AEFC) at the same level of theory have revealed the role of stereochemistry at C position of AEFC in the preferential formation of asymmetric RRS cyclic tripeptide formed by R-, R- and S- stereo isomers of AEFC.

Abstract

Design of biomimetic systems is an alternative method of finding biologically active molecules. Peptides incorporating tetrahydrofuran amino acids (TAA) adopt secondary folding patterns and thus mimic natural peptides. The preferred conformation of TAA derived linear and cyclized peptides depends on the stereochemistry of the tetrahydrofuran (THF) ring. Control of stereochemistry of THF ring in the structure of the linear tripeptide Boc-TAA-Leu-Val- OMe containing (2R,5S)-cis TAA, (2S,5R)-cis TAA, (2R,5R)-trans TAA and (2S,5S)-trans TAA is investigated using structural parameters and energetics data obtained from density functional theory (DFT) based calculations at B3LYP/6-31G(d,p) level of theory. We found that the conformations associated with -, -turn structures are stabilized by intramolecular hydrogen bonding interactions. Kinetic control of reactions leading to intra and inter molecular cyclization of tripeptide TAA-Gly-Gly containing (2S,5R)-cis TAA and (2S,5S)-trans TAA is studied at the same level of theory in gas phase.[1] We observe that kinetic control favors cyclodimerization instead of intramolecular cyclization.