Abstract

Cyclic peptides incorporating a 5 membered ring such as furan mimic naturally occurring cyclic peptides[1]. The preferred conformation of linear and cyclic tripeptides incorporating such sugar amino acids depends on the stereochemistry at the chiral center. Control of stereochemistry at C position of amino ethyl furan carboxylic acid (AEFC) unit in the linear and cyclic tripeptides 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 R-isomer of AEFC unit prefers to form bond with its S-isomer. Thermodynamic analysis revealed that linear tripeptide formed by two R-configured isomers of AEFC and one S-configured isomer of AEFC (RRS or RSR linear) is more stable than that formed by three R-configured isomers of AEFC (RRR linear). It is found that the cyclic tripeptide formed by two R-configured isomers of AEFC and one S-configured isomer of AEFC, i. e., cyclic RRS product is formed with high yield than that formed by three R-configured isomers of AEFC (RRR cyclic) though cyclic RRR trimer is more stable than cyclic RRS trimer. This is substantiated by kinetic control of reactions leading to cyclic tripeptides from linear tripeptides. Using NBO analysis stabilizing interactions in all the linear and cyclic tripeptides are identified. Molecular electrostatic potential (MESP) surfaces of cyclic tripeptides provide insights of intramolecular hydrogen bond interactions. The MESP mapped electron density surfaces have shown the charge distribution around the cyclic peptides.

Abstract

Quantum optimal control theory along with time dependent quantum dynamics is used to control the nuclear motion in the hydrogen bonds of adenine-thymine (A-T) DNA base pair [1]. Optimal infrared laser pulses are designed for selective excitations of (a) single N-H


O hydrogen bond and (b) both N-H


O and N-H


N bonds simultaneously. The conjuagte gradient method is employed to optimize the constructed eld dependent grand functional. Optimal laser elds are realized which give more than 99% population transfer to the preselected vibrational states. The mechanism of population transfer during the vibrational excitation process is investigated by projecting the laser driven nuclear wavefunction onto the vibrational states of the system.

Abstract

Conventionally optimal control theory [1, 2, 3] has been used in the theoretical design of laser pulses through the direct variation of 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, in Genetic Algorithm (GA) approach, a few control parameters are used, which are actually available to the experimentalist. In this work, we investigate 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 this work, 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. The mechanism of population transfer during the excitation process is investigated by projecting the laser driven nuclear wave function onto the eigenstates of the system. We have also investigated the possibility of photodissociation of HF molecule by climbing up the vibrational ladder using this genetic algorithm approach.

Abstract

We provide theoretical insights for the observed preference of cyclodimerization over intramolecular cyclization reactions in tetrahydrofuran amino acid using high level DFT quantum chemical methods, in the gas phase as well as in continuum solvent medium. Thermodynamic results obtained from Hessian calculations indicate the higher stability of intermolecularly cyclized dimer over intramolecularly cyclized monomer. NBO and AIM analysis also support the existence of additional stabilizing hydrogen bond interactions in intermolecularly cyclized products. Further justification for the presence of stabilizing interactions in intermolecularly cyclized products comes from the molecular electrostatic potentials and electron density surfaces.

Abstract

Time dependent quantum dynamics and optimal control theory are used for selective vibrational excitation of the N6-H (amino N-H) bond in free adenine and in the adenine-thymine (A-T) base pair. For the N6-H bond in free adenine we have used a one dimensional model while for the hydrogen bond, N6-H (A)...O4(T), present in the A-T base pair, a two mathematical dimensional model is employed. The conjugate gradient method is used for the optimization of the field dependent cost functional. Optimal laser fields are obtained for selective population transfer in both the model systems, which give virtually 100% excitation probability to preselected vibrational levels. The effect of the optimized laser field on the other hydrogen bond, N1(A)...H- N3(T), present in A-T base pair is also investigated.

Abstract

xDNA constitutes a novel class of size expanded synthetic nucleic acids in which one of the bases of the base pairs is larger than the natural DNA bases. These expanded bases are called x-bases. In this paper, we investigate the hydrogen bonding characteristics and relevant molecular properties of model complexes (xAT)Aun, (xTA)Aun, (xGC)Aun, and (xCG)Aun (n = 4, 6, 8) consisting of xDNA base pairs and gold clusters, in order to study the nature of gold-xDNA binding. We offer detailed characterization of their different aspects, viz., structural, electronic and spectroscopic, effect of gold cluster size, aromaticity, and planarity using quantum mechanics based density functional theory (DFT). Significant charge transfer is seen between the gold clusters and x-base pairs. Gold complexation is found to affect the interbase hydrogen bonding in these complexes. In addition to anchor bonds, XHAu type of hydrogen bonding interactions are also found to contribute to the gold-base pair binding in these complexes.

Abstract

The last two decades have seen increasing interest in the area of controlling dynamics at the atomic level. Among the several approaches used, Optimal Control Theory (OCT) has emerged as a powerful method for designing laser pulses to achieve prescribed dynamical goals. We have used OCT to obtain infrared laser pulses for the selective vibrational excitation of several different systems, from a simple diatomic to triatomics located in complex molecular environments. We use time dependent quantum mechanics to monitor the evolution of the system subject to a varying laser field. We have obtained fields for vibrational control of the diatomic system HF applying OCT using different algorithms, namely an iterative method, conjugate gradient method and genetic algorithms. The time-dependent quantum mechanical propagation of the system is achieved using the split operator form of the time evolution operator together with Fast Fourier transforms and grid methods. For the modelling of FeCO in carboxy-myoglobin, we use a two mathematical dimensional model. Density functional theory is used to obtain the potential energy and dipole moment surfaces of the active site model, while the conjugate gradient method is employed within the OCT optimization procedure to obtain the laser pulses. Optimized laser fields are found which give virtually 100% excitation probability to preselected vibrational levels. A similar application to a hydrogen bonded system of biological significance will also be presented. In all cases, detailed analyses of the field are carried out in terms of its power spectrum and the time variation of the contributions from the frequencies involved.

Abstract

The synthesis of modified versions of DNA is an area that is receiving much attention because of their potential applications in biotechnology and nanotechnology. Recently, Eric Kool et al have re-engineered an expanded version of DNA by pairing size expanded x-bases with normal bases in a complementary manner, which they called as xDNA. xDNA bases are analogues of natural bases that are formed by insertion of benzene ring into the natural bases. Recently, there was arisen a huge interest in conducting properties of metal bound DNA structures. We use quantum chemistry methods to investigate the structural and electronic properties of x-bases and their interaction with gold atoms, in order to explore develop insight into the nature of binding between gold atoms and size expanded DNA.

Abstract

In this paper, we have computationally described the interaction of yDNA bases with small gold clusters through a variety of aspects including geometrical, spectroscopic and energetic one. To get insights in to essential elements of this interaction, the contribution of typical energy interaction components have also been investigated.

Abstract

Predicting the 3D native conformation of a protein given the amino acid sequence is known as protein structure prediction (PSP)problem and is one of the greatest challenge of computational biology. The current work uses a real valued Genetic Algorithm (GA), a powerful variant of conventional GA to simulate the PSP problem. It consists of three evolutionary operators to manipulate the genes and a fitness function based on a simple force field. The individuals of the population correspond to different conformations of the same polypeptide chain, represented by a string of (phi,psi)torsion angles. The conformations are generated under the constraints of Ramachandran plot along with secondary structure information, which are then screened through a set of knowledge based biophysical filters, viz. persistence length and radius of gyration. Only the structures satisfying the filtering criteria are considered for energy minimization using GA. The algorithm has been validated on a set of known globular protein containing 2-4 secondary structure elements. For all the test proteins the algorithm converges rapidly ad the converged structure shows a backbone RMSD (root mean square deviation) or 3-6A as compared to the native structure.