Ab initio stochastic optimization of conformational and many-body degrees of freedom

Moderate to large size molecules in solution have complex energy surfaces due to intramolecular (conformational) and intermolecular (many-body) interactions. The first principles Monte Carlo (FPMC) method, previously shown to effectively locate minimum-energy structures for systems with only many-body complexity, has been extended to address conformational flexibility by adding three new Monte Carlo move types. The primary advantage of the FPMC method is the ability to efficiently locate minimum energy structures of molecules with conformational flexibility in the presence of explicit solvent molecules using highly accurate quantum chemical calculations. The additions to FPMC were validated by studying conformers of glycerol, glyceraldehyde, and a large humic acid monomer unit. The structure of glyceraldehyde in the presence of one and two water molecules was also explored to demonstrate the power of FPMC to study systems with both conformational and many-body degrees of freedom.     

A new ternary Cu (II) complex with 4,7-dimethyl-1,10-phenanthroline and NOO-type tridentate Schiff base ligand: Synthesis,crystal structure,biomacromolecular interactions,and radical scavenging activities

NOO-type tridentate Schiff base, N-salicylidene-2-aminobenzoic acid, (H₂L), and its ternary Cu (II) complex containing H₂L Schiff base and 4,7-dimethyl-1,10-phenanthroline (4,7-dmphen), [Cu(4,7-dmphen)(H₂L)]₂7H₂O, have been synthesized and characterized by CHN analysis, ESI-MS, FTIR, and single-crystal X-ray diffraction techniques. The interaction of alone H₂L Schiff base ligand and ternary Cu (II) complex with biomacramolecules {calf thymus DNA (CT-DNA) and bovine serum albumin (BSA)} has been investigated by electronic absorption and fluorescence spectroscopy. The experimental results indicate that H₂L Schiff base ligand and ternary Cu (II) complex bind to CT-DNA by means of a moderate intercalation mode. Furthermore, the fluorescence quenching mechanism between H₂L Schiff base ligand and ternary Cu (II) complex with BSA possesses a static quenching process. Radical scavenging activity of H₂L Schiff base ligand and ternary Cu (II) complex was measured in terms of EC₅₀, using the DPPH and H₂O₂ methods. Biomacromolecule interactions and scavenging activity studies revealed that ternary Cu (II) complex yielded better results than H₂L Schiff base ligand alone.     

Endomorphin analogues with balanced affinity for bothμ- andδ-opioid receptors

Analogues of endomorphin and tripeptidcs modified at positions 4 and 3,respectively,with various phenylalanine analogues were synthesized and their affinities for opioid receptors were evaluated.Most of the peptides exhibited potentμ-receptor affinity and selectivity,among them,compound 7(Dmt-Pro-Tmp-Tmp-NH_2) exhibited potent affinity for bothμ-andδ-receptors (K_iμ= 0.47 nmol/L,K_iδ= 1.63 nmol/L).     

Many-body optimization using an ab initio monte carlo method

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.