Rational principles of compound selection for combinatorial library design

It is practically impossible in a short period of time to synthesize and test all compounds in any large exhaustive chemical library. We discuss rational approaches to selecting representative subsets of virtual libraries that help direct experimental synthetic efforts for both targeted and diverse library design. For targeted library design, we consider principles based on the similarity to lead molecules. In the case of diverse library design, we discuss algorithms aimed at the selection of both diverse and representative subsets of the entire chemical library space. We illustrate methodologies with several practical examples.     

DFT study on the geometric, electronic structure and Raman spectra of 5,15-diphenylporphine

The ground state geometric, electronic structure and Raman spectra of 5,15-diphenylporphine (H(2)DPP) have been studied using B3LYP/6-31G(d) method and compared with that of well-studied free base porphine (H(2)P) and meso-tetraphenylporphine (H(2)TPP). Calculation shows that 5,15-substitution causes remarkable in-plane distortion, whereas the resulting out-of-plane distortion is negligible. The calculated electronic structure of H(2)DPP is consistent with the absorption spectra compared with H(2)P and H(2)TPP. The calculated vibrational frequencies of H(2)DPP scaled with a single factor of 0.971 agree well with experimental data (the rms error is 8.0 cm(-1)). The assignment of experimental Raman bands of H(2)DPP was discussed on the basis of theoretical calculation and the comparison with that of H(2)P and H(2)TPP. The splitting of some vibrational modes involving the motion of C(m) atom, such as nu(1), nu(8), and nu(10), was observed and was attributed to the diversification of the environment around C(m) atoms. As the shift of absorption peaks, the shift of some structure-sensitive Raman bands of H(2)DPP form that of H(2)TPP and H(2)P was attributed to the in-plane nuclear reorganization (IPNR) induced by phenyl-substitution, though the contribution of nonplanarity mechanism could not be excluded completely.     

An alternative multipolar expansion for intermolecular potential functions

We have derived a new multipolar expansion for intermolecular potential-energy functions with applications in molecular physics, theoretical chemistry, and mathematical physics. The new formulation employs a separation of radial and angular terms with a simple index structure that leads to computational efficiency and ease of physical interpretation. For the case of the Coulomb interaction, we compare the present formulation with two conventional multipole expansions: the Cartesian tensor and the irreducible spherical tensor expansions. The new formalism leads to efficient numerical algorithms that are useful for general applications beyond intermolecular potentials. In addition to the electrostatic Coulomb interaction, we illustrate the formalism with applications to special function theory and a bipolar expansion involved in potential theory.     

Single molecule force spectroscopy reveals the context dependent folding pathway of the C-terminal fragment of Top7

Top7 is a de novo designed protein with atomic level accuracy and shows a folded structure not found in nature. Previous studies showed that the folding of Top7 is not cooperative and involves various folding intermediate states. In addition, various fragments of Top7 were found to fold on their own in isolation. These features displayed by Top7 are distinct from those of naturally occurring proteins of a similar size and suggest a rough folding energy landscape. However, it remains unknown if and how the intra-polypeptide chain interactions among the neighboring sequences of Top7 affect the folding of these Top7 fragments. Here we used single-molecule optical tweezers to investigate the folding–unfolding pathways of full length Top7 as well as its C-terminal fragment (CFr) in different sequence environments. Our results showed that the mechanical folding of Top7 involves an intermediate state that likely involves non-native interactions/structure. More importantly, we found that the folding of CFr is entirely dependent upon its sequence context in which it is located. When in isolation, CFr indeed folds into a cooperative structure showing near-equilibrium unfolding–folding transitions at ∼6.5 pN in OT experiments. However, CFr loses its autonomous cooperative folding ability and displays a folding pathway that is dependent on its interactions with its neighboring sequence/structure. This context-dependent folding dynamics and pathway of CFr are distinct from those of naturally occurring proteins and highlight the critical importance of intra-chain interactions in shaping the overall energy landscape and the folding pathway of Top7. These new insights may have important implications on the de novo design of proteins.

Optical tweezers experiments reveal that the folding of the C-terminal fragment of Top7 (cFr) is context-dependent. Depending on its neighboring sequence, cFr shows very different folding pathways and folding kinetics.      

Effect of diffusion on rates and molecular weights in graft polymerization

A theoretical analysis has been made of the graft polymerization process in terms of the quantitative interrelationship between the initiation rate R_i, the k_p/k_t^1/ ratio of the monomer, the equilibrium solubility M of the monomer in the polymer, the polymer film thickness L, and the diffusivity D of the monomer in the polymer. It is shown how the values of these parameters in any grafting system interact to lead to diffusion-controlled graft polymerization. Whether graft polymerization is diffusion-free or diffusion-controlled depends on the values of K_p, d, k_p/k_p^1/2, and L as gathered in the parameter A = [(K_p/k_t^1/2)R_i, D,/^1/2] L/2. When the values of the various terms are such that A is less than 0.1 (i.e., D is large while R_i, k_p, and L are small), the reaction is diffusion-free. When A is greater than 3 (i.e., D is small while R_i, k_p, and L are large), the reaction is diffusion-controlled. The derived equations showing the relationship between kinetic and diffusional parameters are theoretically applicable to all grafting systems, i.e., for all monomer-polymer combinations under all conditions of reaction temperature, radiation intensity and polymer film thickness. The theoretical analysis has been verified for the rate and degree of polymerization for the radiation-induced graft polymerization of styrene to polyethylene.     

Silicon-29 NMR Study of Alkali-Exchanged NaY Zeolites

High-resolution solid-state ²⁹Si NMR has been applied to the study of partially exchanged Li, K, and Cs NaY zeolites. The order of the ²⁹Si chemical shifts of dehydrated samples is Li, Na-Y < Na-Y < K, Na-Y. The correlation between the ²⁹Si chemical shift and the Li or K loading on Li, Na-Y or K, Na-Y was rationalized in terms of the interaction between the framework and the cations inside the small cages. Because of the restrictive migration of large Cs⁺ ions from the supercages to the small cages, the ²⁹Si chemical shift of Cs, Na-Y was found to be similar to that of Na-Y.     

Synthesis of new 1,3-bis（phenylethynyl）disilazanes

Three new 1,3-bis(phenylethynyl)disilazanes were synthesized from the reaction of 1,3-dichlorodisilazanes with (phenylethy- nyl)lithium,and characterized by infrared (IR) spectra,nuclear magnetic resonance (NMR) and mass spectrometry (MS).     

Synthesis of (4S,9aS)-hexahydro-4-methyl-1H,5H-pyrrolo[2,1-c][1,4]-thiazepine-1,5-dione,A potent angiotensin converting enzyme inhibitor

Synthesis of (4S,9aS)-hexahydro-4-methyl-1H,5H-pyrrolo[2,1-c][1,4]thiazepine-1,5-dione, an orally active potent angiotensin converting enzyme inhibitor is described.     

Theoretical formalism and experimental verification of line shapes of NMR intermolecular multiple-quantum coherence spectra

Although the theories and potential applications of intermolecular multiple-quantum coherences (iMQCs) have been under active investigations for over a decade, discussion of iMQC NMR signal formation was mainly confined in the time domain. In this paper, a full line-shape theory was developed to describe iMQC signals in the frequency domain. Relevant features of the line shape, such as peak height, linewidth, and phase, were investigated in detail. Predictions based on the theory agree well with experimental and simulated results. Since radiation-damping effects always couple with iMQCs in highly polarized liquid-state NMR systems, and strongly radiation-damped signals have many spectral characteristics similar to those of iMQCs, a detailed comparison was also made between them from different spectral aspects. With detailed comparison of peak height, linewidth, and phase, this work demonstrates that the iMQC and radiation-damping phenomena result from two completely different physical mechanisms despite that both present similar signal features and coexist in highly polarized liquid-state NMR systems.     

Bound states and scattering resonances of OH(A)-He

The OH-He complex has been observed using laser excitation of the A 2sigma+-X 2pi transition. The bands of the complex were close to the monomer rotational lines that terminate on the n = 0, 1, and 2 levels of OH(A). The unresolved band associated with He.OH (A,n=0) was redshifted from the OH parent line by 1.6 cm(-1), providing a direct measurement of D0'-D0". The complex features associated with n = 1 and 2 were identified as scattering resonances. They have been assigned by comparison with resonance structures derived from close-coupling calculations. The ab initio potential energy surface of H.-S. Lee, A.B. McCoy, R.R. Toczylowski, and S.M. Cybulski, [J. Chem. Phys. 113, 5736 (2000)] was used in these calculations. The level of agreement between the observed and predicted resonances indicated that the ab initio surface is reasonably accurate.