Spinodal decomposition in a model colloid-polymer mixture in microgravity.

We study phase separation in a deeply quenched colloid-polymer mixture in microgravity on the International Space Station using small-angle light scattering and direct imaging. We observe a clear crossover from early-stage spinodal decomposition to late-stage, interfacial-tension-driven coarsening. Data acquired over 5 orders of magnitude in time show more than 3 orders of magnitude increase in domain size, following nearly the same evolution as that in binary liquid mixtures. The late-stage growth approaches the expected linear growth rate quite slowly.

Antiangiogenic agents: studies on fumagillin and curcumin analogs.

Cancer is a general term used to describe many disease states, each of which are characterized by abnormal cell proliferation. The causes which bring about this abnormal cellular behavior are specific to each type of cancer. The success of tumor-targeted therapy is limited by this diversity. One common denominator for all types of cancer is the requirement of a suitable blood supply. Therefore, tumor vasculature has emerged as a potential target for therapeutic intervention. New blood vessel growth from preexisting vasculature stimulated by biochemical signals is termed angiogenesis. Tumor masses require a constant supply of oxygen and nutrients, and a means of efficient waste removal to ensure sustained development. Diffusion from nearby capillaries can supply adequate nutrition for tumors less than 2 mm in size, but for continued growth the tumors must develop their own blood supply. Alteration of the delicate balance of angiogenic stimulating factors and angiogenic inhibitors results in the phenotypic change from quiescence to active endothelial proliferation. To date, this angiogenic switch is not completely understood. The goal of antiangiogenic therapy is to interfere with these mechanisms and prevent tumor cells from developing a viable blood supply. Fumagillin is a naturally occurring antifungal agent. Curcumin is a natural product isolated from the spice turmeric. Both compounds have been shown to have antiangiogenic properties in vitro and in vivo. This paper describes efforts to design and prepare fumagillin and curcumin analogs and evaluate their corresponding antiangiogenic activities.

Molecular mechanics force-field development for amino acid zwitterions.

Understanding the conformational flexibility of amino acid zwitterions (ZWs) and their associated conformational energies is crucial for predicting their interactions in biological systems. Gas-phase ab initio calculations of ZWs are intractable. Molecular mechanics (MM), on the other hand, is able to handle large systems but lacks the necessary force field parameters to model ZWs. To develop force field parameters that are able to correctly model ZW geometries and energetics we used a novel combinatorial approach: amino acid ZWs were broken down structurally into key functional components, which were parameterized separately. Møller-Plesset second-order perturbation calculations on small carboxylates, on the glycine cation, and on novel hydrogen bonded systems, coupled with available experimental data, were used to generate MM3(2000) ZW parameters (Allinger N. L.; Yuh, Y. H.; Lii, J.-H. J Am Chem Soc 1989, 111, 8551). The MM3 results from this combinatorial approach gave geometries that are in good agreement with neutron diffraction experiments, plus their frequencies and energies appear to be reasonably modeled. Current limitations and future development of MM force fields are discussed briefly.

Ab initio and molecular mechanics (MM3) calculations of protonated-neutral diamine hydrogen bonds.

Ab initio calculations of cation-neutral diamine complexes have been carried out at the MP2/6-311+G** level. The geometry and energetics of the charge-reinforced hydrogen bond are analyzed with respect to the alkyl substitution of both the protonated and neutral nitrogen atoms, and these results have been used to improve the quality of the MM3(2000) force field. In addition, specialized hydrogen bond parameters optimized for MM3(2000) are presented. These parameters allow very accurate gas-phase modeling of the charge-neutral diamine environment. Molecular mechanics calculations can model effectively protonated amine-neutral amine hydrogen bonds in the gas phase and solution (continuum dielectric) through a combination of charge-dipole interactions and explicit hydrogen-bonding terms.

Density functional and Ab initio studies on N-acetylduocarmycin SA: insight into its DNA interaction properties.

Density functional (DF) and Møller-Plesset second order perturbation (MP2) calculations were carried out on N-acetylduocarmycin SA (N-Ac-DSA), an analogue of a series of potent antitumor antibiotics that include the duocarmycins. These computational methods were used to investigate the degree of ground state destabilization of duocarmycins that would result upon binding to DNA. Ground state destabilization has been proposed as the origin of the ligand's enhanced rate of alkylation by more than a millionfold. The conformations of the 'Unbound' and 'DNA-Bound' N-Ac-DSA were generated using available geometric data for duocarmycin SA. Specifically, the dihedral angles chi1/chi2 were locked at 6.9 degrees/4.5 degrees for the Unbound and 22.0 degrees/11.0 degrees for the Bound form. The structures were optimized using DF theory, with subsequent MP2 calculations to improve the electronic energies. All of the calculations were performed on the unprotonated (1) as well as the C6-carbonyl protonated form (2). The results showed that the ground state destabilization energies of the Unbound and Bound forms, for the unprotonated and protonated series, were fairly small (< 0.8 kcal/mol). Similarly, the difference in the electronic nature of the Unbound and Bound forms, as indicated by changes in bond lengths and charge density, were also small. In summary, it appears that twisting of two key torsional angles, the concomitant ground state destabilization, and C6-carbonyl protonation may not fully account for the significant rate increase of adenine-N3 alkylation upon binding to DNA.

Molecular Mechanics (MM3) Calculations on Oxygen-Containing Phosphorus (Coordination IV) Compounds.

An MM3 force field has been developed for small oxygen-containing phosphorus (coordination IV) compounds. Experimental electron and neutron diffraction, X-ray, and infrared spectral data were utilized in parametrization when available. Results from previous ab initio calculations at both the restricted Hartree-Fock (RHF) and second-order Møller-Plesset (MP2) levels of theory with the standard 6-31G basis set supplemented missing structural data, rotational profiles, and vibrational frequencies. Negative hyperconjugation (the anomeric effect) affects the structures and energies of the molecules under study which contain one or more sp(3)-hybridized oxygen atoms. Natural bond order (NBO) analysis was helpful in identifying the key orbital interactions involved in this effect.

MM3(96) parameterization for camptothecin analogs: an ab initio and molecular mechanics study.

Torsional parameters for MM3(96) were derived for the missing atom types present in the natural product camptothecin (CPT). Potential energy curves were calculated via ab initio calculations on representative compounds for dihedral angles containing these missing parameters. Gaussian 92 at the restricted Hartree-Fock level of theory using the standard 6-31G** and 4-31G** basis sets, was used for all the quantum-mechanics calculations. Missing MM3 torsional terms were obtained by optimizing the V1, V2 and V3 parameters such that MM3 could reproduce the ab initio torsional profile. MM3 calculated molecular structures that compare well with the ab initio results. Using the newly developed parameters, conformational analyses and QSAR studies of camptothecin analogs were undertaken. MM3 predicts two distinct 'boatlike' conformations for the alpha-hydroxy lactone moiety. The low-energy lactone conformation predicted by MM3 is in general agreement with reported X-ray crystal structures of CPT iodoacetate and 7-ethyl-10-(4-piperidino)piperidinylcarbonyloxy CPT HCl as well as the ab initio structure of a CPT-like alpha-hydroxy lactone.

Comparative molecular field analysis and molecular modeling studies of 20-(S)-camptothecin analogs as inhibitors of DNA topoisomerase I and anticancer/antitumor agents.

Conformational studies and comparative molecular field analysis (CoMFA) were undertaken for a series of camptothecin (CPT) analogs to correlate topoisomerase I inhibition with the steric and electrostatic properties of 32 known compounds. The resulting CoMFA models have been used to make predictions on novel CPT derivatives. Using the newly derived MM3 parameters, a molecular database of the 32 CPT analogs was created. Various point atomic charges were generated and assigned to the MM3 minimized structures, which were used in partial least-squares analyses. Overall, CoMFA models with the greatest predictive validity were obtained when both the R- and S-isomers were included in the data set, and semiempirical charges were calculated for MM3 minimized low-energy lactone structures. A cross-validated R2 of 0.758 and a non-cross-validated R2 of 0.916 were obtained for MM3 minimized structures with PM3 ESP charges for the 32 CPT analogs. The derived QSAR equations were used to assign topoisomerase I inhibition values for compounds in this study and compounds not included in the original data set. Prior to its appearance in the literature, an IC50 of 103 nM was predicted for the 10,11-oxazole derivative. This CoMFA predicted value compared favorably with the recently reported value of 150 nM. The CoMFA model was also evaluated by predicting the activities of recently reported 11-aza CPT and trione derivatives. The predicted activity (IC50 = 249 nM) for 11-aza CPT compared well with the reported value of 383 nM.

Generation of large-diameter diffractive elements with laser pattern generation.

We describe the design and construction of a high-precision laser writing machine for the direct generation of large-diameter rotationally symmetric diffractive optics with continuous profiles in photoresist. The photoresist profile can be used as a replication master surface or etched into a silica substrate. Machine design methodology, as well as qualification of performance, is provided. Test results for an f/2 100-mm clear-aperture diffractive lens directly etched into a silica substrate are presented. Diffraction efficiency as a function of zone spacing and wave-front performance are given.

Xylanase homology modeling using the inverse protein folding approach.

Xylanase has been used in wood pulp bleaching in an effort to reduce chlorine release into the environment and pollution associated with paper production. The three-dimensional structure of xylanase is important to enable better understanding of the enzyme mechanism and to help design a more thermostable xylanase mutant. At the time this work was begun, there was no sequence homologous protein available for traditional sequence-based homology modeling. In order to circumvent this problem, the inverse protein folding approach was undertaken to find a suitable template structure. Model structures of Bacillus circulans xylanase were built based on the data-base search results of related proteins. The model structures were refined and compared to the recently solved xylanase X-ray crystal structure. The overall structural similarity between the theoretical model and experimental structure demonstrate the usefulness of this approach. Disagreement in folding topology, however, warrants further research into the inverse protein folding approach.

Computational modeling of a putative fetal alcohol syndrome mechanism.

Fetal alcohol syndrome (FAS) refers to a pattern of birth defects occurring in a subpopulation of children born to women who consume alcohol during pregnancy. The significant medical, social, and economic impact of FAS is increasing. Particularly hard-hit are African-American and native-American women and children. Over the past two decades, basic and clinical research produced voluminous data on ethanol effects on developing organisms. In 1991, Duester and Pullarkat proposed that competition of ethanol with retinol at the alcohol dehydrogenase (ADH) binding site formed the basis of the FAS mechanism. This competition adversely affects the developing fetus caused by deregulation of retinoic acid (RA) homeostasis essential for proper fetal tissue development. Stated concisely, the FAS hypothesis is: 1. Class I ADH catalyzes the rate-limiting step in oxidation of retinol (ROH) to RA, and ethanol (ETOH) to acetic acid, thus establishing competition for ADH between ROH and ETOH. 2. RA is required as a signal molecule for cell differentiation critical for normal fetal morphogenesis. 3. ADH binds ingested ETOH, thus deregulating RA homeostasis leading to improper RA signal transduction. Preliminary results from molecular modeling studies of ROH-ADH and ETOH-ADH structures, and physiologic pharmacokinetic modeling confirm the hypothesis with remarkable fidelity.

Molecular modeling studies of some choline acetyltransferase inhibitors.

Choline acetyltransferase (ChAT) inhibitors related to trans-1-methyl-4- (1-naphthylvinyl)-pyridinium (NVP+) have been assumed to depend upon a nearly or completely planar conformation for their enzyme-inhibitor interaction. In an effort to investigate the geometries and preferred conformations for these compounds, geometry optimizations using the semiempirical molecular orbital method AM1 and a modified version of the molecular mechanics method MM2(92) have been carried out. The results indicate that the active inhibitors are either planar or nearly coplanar, lying in relatively flat potential wells in the vicinity of the corresponding planar structures. When nonplanarity is favored, one ring is twisted out of the plane by approximately 30 degrees. Where steric features significantly deter assumption of a nearly planar conformation, the analogs are inactive. The inactivity of analogs bearing tricyclic aryl groups appears to result from bulk-related hindrance to ChAT receptor binding rather than lack of coplanarity.

Computer-assisted molecular modeling: indispensable tools for molecular pharmacology.

Ball-and-stick mechanical models, typically associated with chemists, have been helpful in understanding structural problems and the relationship between structure and biologic activity. With progress in computer speed, graphics performance, and software innovation, molecules of biological interest can be subjected to rigorous calculations. Computational chemistry and biology are rooted in the belief that theoretical physics can be used to calculate accurate molecular structures. Although in its infancy, computer-assisted molecular modeling is gaining attention and acceptability as an increasing number of researchers turn their attention toward rational molecular design. The trend to use theoretical methods can be traced to the greater availability of computer graphics work-stations, decreasing computer costs, faster central processing units, more robust algorithms, and "user-friendly" software codes. Every major pharmaceutical company has invested in these resources to reduce the time it takes to design and develop pharmaceutical agents. Because of the vast financial and manpower investments needed to introduce a single drug, medicinal chemists and pharmacologists are interested in understanding and predicting drug action at the molecular level. Although drug action is still poorly understood, molecular modeling should reduce some of the labor in the development of pharmaceutical agents.

Requirements for high affinity binding of glycine analogs to the glycine site of the NMDA receptor complex.

Correlation of the isopotential contours of the optimized conformations of a series of alpha-amino acids, in their neutral and zwitterionic forms, with their potencies to inhibit [3H]glycine binding and to enhance [3H]10,11-dihydro-5-methyl-5H-dibenzo[a,d]cyclohepten-5,10-imine ([3H]MK-801) binding, leads to the following conclusions: (a) steric congestion at the amino group is detrimental to binding potency; (b) a zwitterionic amino acid is required for high affinity to the receptor; (c) a conformation in which the carboxylate group is at a 90 degrees dihedral angle to the ammonium nitrogen is preferred for high affinity; and (d) placing the carbon backbone of the zwitterionic alpha-amino acid, in its preferred conformation, above the plane defined by the ammonium nitrogen and the carboxylate oxygen atoms, and viewing the molecule along the nitrogen to carboxylate carbon axis, there is a space forbidden to the ligand (receptor-required-space) to the left.

Influence of temperature on diffractive lens performance.

The thermal properties of lenses play an important role in the performance of optical systems. We discuss the effects of uniform temperature changes and thermal gradients on diffractive lens performance. Comparisons are made between the thermal sensitivity of refractive and diffractive lenses. Useful design equations are presented that describe focal length, phase coefficients, and diffraction efficiency as functions of temperature. We present important thermal data for a number of lens materials. The optothermal expansion coefficient is used to design athermalized lenses that combine refractive and diffractive surfaces.

Do interhelical side chain-backbone hydrogen bonds participate in formation of leucine zipper coiled coils?

The leucine zipper proteins are a group of transcriptional regulators that dimerize to form a DNA binding domain. It has been proposed that this dimerization results from the hydrophobic association of the alpha-helices of two leucine zipper monomers into a coiled coil. We propose a model for a coiled coil based on a periodic hydrophobic-hydrophilic amino acid motif found in the leucine zipper regions of 11 transcriptional regulatory proteins. This model predicts the symmetrical formation of secondary hydrogen bonds between the polar side chains of one helix and the peptide carbonyls of the opposite chain, supplementing the interactions between hydrophobic side chains. Physical modeling (CPK) and in vacuo molecular mechanics calculations of the stability of the GCN4 leucine zipper coiled coil configured in accordance with this model demonstrate a greater stability for this conformer than for a conformer configured according to a current hydrophobic model. Molecular dynamics simulations show similar stability of the two models in vacuo but a higher stability of the hydrophobic model in water.

Characteristics of chemical binding to alpha 2u-globulin in vitro--evaluating structure-activity relationships.

alpha 2u-Globulin (alpha 2u) has been shown to accumulate in the kidneys of male rats treated with 2,2,4-trimethylpentane (TMP). 2,4,4-Trimethyl-2-pentanol (TMP-2-OH), a metabolite of TMP, is found reversibly bound to alpha 2u isolated from the kidneys of these treated rats. The objectives of the following study were to characterize the ability of [3H]TMP-2-OH to bind to alpha 2u in vitro and to determine whether other compounds that cause this protein to accumulate have the same binding characteristics. Although compounds that have been shown to cause the accumulation of alpha 2u in male rat kidneys compete in vitro with [3H]TMP-2-OH for binding to alpha 2u, they do so to varying degrees. The binding affinity (Kd) of the [3H]TMP-2-OH-alpha 2u complex was calculated to be on the order of 10(-7) M. The inhibition constant values (Ki) determined for d-limonene, 1,4-dichlorobenzene, and 2,5-dichlorophenol were all in the range 10(-4) M, whereas the Ki values for isophorone, 2,4,4- or 2,2,4-trimethyl-1-pentanol, and d-limonene oxide were determined to be in the range 10(-6) and 10(-7) M, respectively. TMP and 2,4,4- and 2,2,4-trimethylpentanoic acid did not compete for binding. This suggests that other factors, besides binding, are involved in the accumulation of alpha 2u. In this study the ability of a chemical to bind to alpha 2u was used as a measure of biological activity to assess structure-activity relationships among the chemicals tested and known to cause the accumulation of alpha 2u. The results so far suggest that binding is dependent on both hydrophobic interactions and hydrogen bonding.

Antitumor agents. 113. New 4 beta-arylamino derivatives of 4'-O-demethylepipodophyllotoxin and related compounds as potent inhibitors of human DNA topoisomerase II.

A number of 4'-O-demethylepipodophyllotoxin derivatives possessing various 4 beta-N-, 4 beta-O- or 4 beta-S-aromatic rings have been synthesized and evaluated for their inhibitory activity against the human DNA topoisomerase II as well as for their activity in causing cellular protein-linked DNA breakage. The results indicated, that for DNA topoisomerase II, a basic unsubstituted 4 beta-anilino moiety is structurally required for the enhanced activity. Substitution on this moiety with CN, COOCH3, COOC2H5, OH and COOCH3, OCH3, COCH3, CH2OH, OCH2O, OCH2CH2O, phenoxy, morpholino, NO2, and NH2 either at the para and/or the meta position yielded compounds which are as potent or more potent than etoposide. Substitution with COOC2H5 and OH at the ortho position afforded inactive compounds. Replacement of the aryl nitrogen with oxygen or sulfur gave compounds which are much less active or inactive. However, replacement of the phenyl ring with a pyridine nucleus furnished compounds which are as active or slightly more active than etoposide. There is a lack of correlation between the ability of these compounds in inhibiting DNA topoisomerase II and in causing protein-linked DNA breaks.

Effects of axial and radial gradients on Cooke triplets.

This study investigates the role of gradient-index materials in the design of Cooke triplets for use as 35-mm format photographic objectives. Cooke triplet designs are presented with different types of gradient-index profiles. Both linear axial and shallow radial gradients are shown to provide effective control of spherical aberration and astigmatism. In particular, a Cooke triplet with a combination of both linear axial and radial gradients attains performance comparable to a six-element double Gauss lens. In virtually all cases, the use of gradient-index components improves the Cooke triplets' performance significantly.

Conformational analysis and molecular modeling of 1-phenyl-, 4-phenyl-, and 1-benzyl-1,2,3,4-tetrahydroisoquinolines as D1 dopamine receptor ligands.

Conformational studies on a series of 1-phenyl-, 4-phenyl-, and 1-benzyl-1,2,3,4-tetrahydroisoquinolines that possess an identical substituent pattern to the prototypical D1 dopamine receptor antagonist SCH23390 [(R)-(+)-7-chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5- tetrahydro-1H-3-benzazepine (1)] were performed with use of molecular mechanics calculations [MM2(85), with newly developed aromatic halide bending and torsional parameters that are now incorporated into MM2(87)], single-crystal X-ray analysis, and high-field NMR spectroscopy. The synthesis and biological testing of compounds 2-7 has been previously reported. The test compounds were compared both quantitatively and graphically to compound 1. Calculations on both the free-base and protonated forms of each compound were carried out. To insure that conformation space was adequately sampled, the test compounds were energy minimized from different starting geometries; ring inversion of the heterocycle was employed, as were dihedral driver calculations on the phenyl or benzyl rings. For N-methyl-6-chloro-7-hydroxy-1-phenyl-1,2,3,4-tetrahydroisoquinoline (2), it was determined that the torsion angle tau(C8a-C1-C12-C17) had energy minima at approximately 60 degrees and 240 degrees. This finding was corroborated by NMR studies that indicated a dramatic upfield chemical shift of ArH8 after ring cyclization. The nitrogen lone pair or hydrogen vector was approximately orthogonal to the plane of the substituted aromatic ring in the tetrahydroisoquinolines; this explained the upfield chemical shift of the vicinal chiral proton (H1). In all instances, the 6-membered heterocyclic ring in the energy-minimized structures preferred the half-chair conformation with the phenyl rings pseudo-equatorial. Distance comparisons of the proposed pharmacophoric atoms (Cl, N, O, centroid of the phenyl or benzyl ring) showed that the phenyl or benzyl centroid to ammonium H distance, Cl to N distance, and distance of the nitrogen above or below the plane of the isoquinoline aromatic ring are the distances most highly correlated with biological activity (r = 0.82, 0.75, 0.81, respectively). Resolution and single-crystal X-ray analysis of compound 2 showed the most active enantiomer to possess the S absolute configuration, in contrast to the benzazepine (R)-1. Least-squares fitting of the energy-minimized structures with SYBYL molecular modeling software showed (S)-(+)-2, rather than (R)-(-)-2, gave a better fit to (R)-1. Volume determinations derived from SYBYL multifit analyses aided in receptor mapping to qualitatively describe areas of "active" pharmacophore space as well as areas of "inactive" substituent space.(ABSTRACT TRUNCATED AT 400 WORDS)