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PubMed1982

Electron-capture, capillary column gas chromatographic determination of low-molecular-weight diols in serum.

Research on alcoholism has revealed that concentrations of 1,2-propanediol, d,1-2,3-butanediol and meso-2,3-butanediol may be greater in the serum of chronic alcoholics than in the serum of social drinkers and nondrinkers. In connection with one of these studies, we developed methodology to determine these diols at the micromolar levels in 500 serum samples. The procedure consisted primarily of extraction of the serum with acetonitrile containing internal standard. The extract was then concentrated to dryness and reacted with p-bromophenylboric acid. The reaction mixture was injected into a gas chromatograph fitted with a capillary column and an electron-capture detector. The total coefficients of variation were best for 1,2-propanediol, 6.82 and 10.00%, and worst for d,1-2,3-butanediol, 13.64 and 19.22%. The observed means for the analytes were all within 10% of the spiked level.

Alcoholism↗
PubMed2000

Capillary electrophoretic separation of vitamins in sodium dodecyl sulfate containing buffers with lower aliphatic alcohols and n-hexane as organic modifiers.

The effect of lower organic alcohols as co-surfactants (methanol, ethanol, n-propanol, isopropanol, propanediol, n-butanol and isoamylalcohol) and n-hexane as an organic modifier in 12.5 mol/l phosphate buffer with varying SDS concentration was investigated using a set of vitamins and p-hydroxybenzoic acid as the test mixture. It was demonstrated that optimum separations can be achieved particularly at high concentrations of the surfactant; the selectivity can be changed by adding a co-surfactant; while propanol and isopropanol show the same properties as co-surfactants, the most efficient alcohols were isoamylalcohol and propanediol. n-Butanol was capable of selective separation of p-hydroxybenzoic acid in the test mixture. Addition of ethanol appears most effective at higher concentrations (while all the other alcohols are effective already at 5% concentration, the best results with ethanol were obtained when it constituted 20% of the background electrolyte). 5% Concentration of methanol resulted in poor separation of the test mixture, however if 300 microl/10 ml of hexane were added to 20 mmol/l SDS containing phosphate buffer, the resulting separation was practically the same as with 50 mmol/l SDS.

Alcohols↗
PubMed2001

Preparation and characterisation of a range of diclofenac salts.

Physicochemical properties of diclofenac salts prepared using eight different counterions and including five novel salts, obtained with the bases 2-amino-2-methyl-1,3-propanediol, 2-amino-2-methylpropanol, tert-butylamine, benzylamine and deanol, were compared. Four of the bases used to prepare these salts were related in their chemical structure, differing only in the number of hydroxy groups. Characterisation techniques included X-ray diffraction, differential scanning calorimetry, thermogravimetric analysis, thermomicroscopy, Karl Fischer titration, FT-IR spectroscopy and elemental analysis. In the case of salts prepared from 2-amino-2-methylpropanol and benzylamine, two polymorphic forms of each salt were identified. For the 2-amino-2-methyl-1,3-propanediol salt, a pseudopolymorphic form was identified. The aqueous solubilities of the salts studied ranged from 3.95 mM (tris(hydroxymethyl)aminomethane salt) to 446 mM (deanol salt), corresponding to a 113-fold difference in solubility. The solubility of diclofenac deanol was higher than the solubilities for diclofenac salts reported earlier. Correlation was found between the inverse of the salt melting point and the logarithm of salt solubility. A log-log relationship was observed between salt solubility and hydrogen ion concentration in the salt solution. Relationships between the properties of the salt-forming agents and those of the resulting diclofenac salts were explored. Reasonable correlation was found between the free base melting point and the salt melting point.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed1990

Analysis of the thermal stability of type II collagen in various solvents used for reversed-phase high performance chromatography.

The thermal stability of type II collagen in various solvents is shown to depend on the ability of the solvent to form hydrogen bonds. Mixtures of water with 1-propanol, 2-propanol, 1,2-propanediol, tetrahydrofuran and acetonitrile effect the stability of the triple helix differently. The temperature of the triple helix coil transition of type II collagen in 50(v/v)% solvent mixture in 0.1% trifluoroacetic acid ranges from 34 degrees C for 1,2-propanediol to 22.5 degrees C for acetonitrile, compared to 38 degrees C in 0.1% trifluoroacetic acid and 41.5 degrees C at neutral pH. There is no correlation between the dielectric constants of the solvents and the decrease in thermal stability, indicating that electrostatic interactions play only a minor role in the stability of the triple helix. Acetonitrile and tetrahydrofuran destabilize the triple helix more than the solvents containing hydroxyl groups. For reversed-phase high performance chromatography 2-propanol is the solvent of choice, but temperature control is very important, because the interaction of the triple helix with the column matrix leads to an additional destabilization of the triple helix beyond the destabilization effect of the solvent. In acetonitrile, a solvent commonly used for reversed-phase high performance chromatography, the triple helix is completely denatured when eluted from a C18 column at room temperature.

Animals↗
PubMed2000

Effects of boron derivatives on extracellular matrix formation.

Boric acid solution (3%) dramatically improves wound healing through action on the extracellular matrix, a finding that has been obtained in vitro. Consequently, investigations are presently underway to produce boronated compounds having a therapeutical effectiveness similar to that of boric acid. On the basis of experimental results obtained with boric acid, we examined the effects of boron derivatives on extracellular matrix formation and degradation and analyzed their potential toxicity by using two biological models (chick embryo cartilage and human fibroblasts). The four boron derivatives tested in this study (triethanolamine borate; N-diethyl-phosphoramidate-propylboronique acid; 2,2 dimethylhexyl-1,3-propanediol-aminopropylboronate and 1,2 propanediol-aminopropylboronate) mimicked the effects of boric acid. They induced a decrease of intracellular concentrations in extracellular matrix macromolecules (proteoglycans, proteins)-associated with an increase of their release in culture medium and stimulated the activity of intra- and extracellular proteases. Similarly to boric acid, these actions occurred after exposure of the cells to concentrations of all boron derivatives without apparent toxic effects. The compounds were found to be more toxic than boric acid itself when concentrations were calculated according to their molecular weight. Nevertheless, these in vitro preliminary results demonstrate effects of boron derivatives that may be of therapeutic benefit in wound repair.

Animals↗
PubMed1990

Lateral proton conduction in monolayers of phospholipids from extreme halophiles.

Studies have been carried out on the lateral proton conductance properties of monolayers of the major and minor phospholipids of extremely halophilic archaebacteria, 2,3-diphytanyl-sn-glycero-1-phospho-3'-sn-glycerol 1'-phosphate (PGP) and 2,3-diphytanyl-sn-glycero-1-phospho-3'-sn-glycerol (PG), respectively, as well as on their respective deoxy analogues: 2,3-diphytanyl-sn-glycero-1-phospho-1'-propanediol 3'-phosphate (dPGP), 2,3-diphytanyl-sn-glycero-1-phospho-1'-1',3'-propanediol (dPG), and 2,3-diphytanyl-sn-glycero-1-phospho-1'-propanol (ddPG). Lateral proton conduction was found to occur with monolayers of all ether phospholipids examined at reduced surface pressure (pi greater than 25 mN/m) on subphases of low (1 mM) and high (4 M) ionic strength. Proton conduction was also detected in highly condensed monolayers (greater than 35 mN/m) of the naturally occurring phospholipids (PGP, PG) but was abruptly terminated in tightly packed monolayers (greater than 35 mN/m) of the corresponding deoxy compounds (dPGP, dPG, ddPG) on subphases with low ionic strength. conduction did occur, however, along monolayers of the deoxy compounds at high surface pressure when spread on a subphase of high ionic strength (4 M). The abrupt termination of conduction with monolayers of the deoxy compounds at low ionic strength cannot be attributed to a lipid phase transition or to changes in the lateral fluidity of the monolayers, nor was the pK of the fluorescent interfacial proton indicator affected at high surface pressures.(ABSTRACT TRUNCATED AT 250 WORDS)

Fluorescence↗
PubMed1981

Esterification of terminal phosphate groups in nucleic acids with sorbitol and its application to the isolation of terminal polynucleotide fragments.

The exposure of mono- and polynucleotides to 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide and high concentrations of sorbitol results in the esterification of their monosubstituted phosphate groups. The presence of the sorbitol moiety permits these derivatives to bind strongly at pH 8.7 to columns of chromatographic supports containing the dihydroxyboryl group and to be subsequently released by elution with buffers at pH 5.5. The procedure constitutes a method for the isolation of polynucleotide fragments arising from the terminals of nucleic acids. A new method for the preparation of the chromatographic supports involves the synthesis of the 1,3-propanediol cyclic ester of m-[[3-(N-succinimidoxycarbonyl)propanoyl]amino]benzeneboronic acid and its condensation with aminoethylcellulose or amino-ethylpolyacrylamide. The reagent is readily prepared by reaction of N-[m-(dihydroxyboryl)phenyl)]succinamic acid with 1,3-propanediol to protect the boronate moiety followed by esterification with N-hydroxysuccinimide in the presence of dicyclohexylcarbodiimide.

Animals↗
PubMed1981

Motions and interactions of phospholipid head groups at the membrane surface. 2. Head groups with hydroxyl groups.

A set of phospholipids with zero, one, or two hydroxyl groups at various positions in the head group were synthesized to approach the question of hydrogen bonding at the surface of phospholipid membranes. These lipids had as head groups the alcohols propanol, ethanediol, 1,3-propanediol, and glycerol esterified to the phosphate. The four different properties of these lipids that were studied were the following: phase transition temperatures, packing properties in monolayers, the relative rates of head-group motions, and the "ordering" of the head group. The gel-to-liquid-crystalline phase transition temperatures of these derivatives were measured by differential scanning calorimetry, and the effect of hydroxyl group addition was found to be small. The phase properties were examined with phosphorus-31 NMR, and all lipids formed normal bilayer phases in aqueous mixtures. Measurement of the surface pressure-area diagrams for monolayers of these lipids showed that incorporation of a hydroxyl group into the head group had a "condensing" effect. This effect was dramatic and was attributed to the formation of hydrogen bonds within the plane of the lipid surface. These lipids were synthesized with deuterium labels on essentially every carbon segment in the head group. Measuring the 2H NMR spin-lattice (T1) relaxation time allowed a determination of the relative rates of head-group segmental motions. The addition of hydroxyl groups to the propyl head-group "skeleton" substantially reduced the rates of motion in both the liquid-crystalline and gel states. The head groups could be ordered in terms of increasing rigidity as propanol (0 -OH) less than 1,3-propanediol (1 -OH) less than ethanediol (1 -(OH) less than glycerol (2 -OH). This trend was observed for labels attached to all of the head-group carbon segments of the lipids in this set. The rates of motion of the different segments within the ethanediol or glycerol head groups were almost identical, whereas those of the propyl head group increased as one progressed toward the free end of the head group. The average activation energy for the motions involved in T1 relaxation increased upon introduction of a hydroxyl group. Measurement of the deuterium residual quadrupole splittings showed that the initial PO2--O--CD2-- segments of the hydroxyl-containing head groups have very similar ordering properties which differed distinctly from those of the propyl head group. Thus, the introduction of one hydroxyl group appears to alter the head-group conformation to a specific conformation which is shared by all of these hydroxyl group containing head groups.

Alcohols↗
PubMed2003

Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates.

The haloalkane dehalogenases are detoxifying enzymes that convert a broad range of halogenated substrates to the corresponding alcohols. Complete crystal structures of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB), and complexes of LinB with 1,2-propanediol/1-bromopropane-2-ol and 2-bromo-2-propene-1-ol, products of debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, were determined from 1.8 A resolution X-ray diffraction data. Published structures of native LinB and its complex with 1,3-propanediol [Marek et al. (2000) Biochemistry 39, 14082-14086] were reexamined. The full and partial debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, conformed to the observed general trend that the sp(3)-hybridized carbon is the predominant electrophilic site for the S(N)2 bimolecular nucleophilic substitution in dehalogenation reaction. The 2-bromo-2-propene-1-ol product of 2,3-dibromopropene dehalogenation in crystal was positively identified by the gas chromatography-mass spectroscopy (GC-MS) technique. The 1,2-propanediol and 1-bromopropane-2-ol products of 1,2-dibromopropane dehalogenation in crystal were also supported by the GC-MS identification. Comparison of native LinB with its complexes showed high flexibility of residues 136-157, in particular, Asp146 and Glu147, from the cap domain helices alpha(4) and alpha(5)('). Those residues were shifted mainly in direction toward the ligand molecules in the complex structures. It seems the cap domain moves nearer to the core squeezing substrate into the active center closer to the catalytic triad. This also leads to slight contraction of the whole complex structures. The flexibility detected by crystallographic analysis is in remarkable agreement with flexibility observed by molecular dynamic simulations.

Binding Sites↗
PubMed2005

Role of loop residues and cations on the formation and stability of dimeric DNA G-quadruplexes.

Formation of guanine-quadruplexes by four DNA oligonucleotides with common sequence dG4-loop-dG4 has been studied by a combination of NMR and UV spectroscopy. The loops consisted of 1',2'-dideoxyribose, propanediol, hexaethylene glycol, and thymine residues. The comparison of data on modified and parent oligonucleotides gave insight into the role of loop residues on formation and stability of dimeric G-quadruplexes. All modified oligonucleotides fold into dimeric fold-back G-quadruplexes in the presence of sodium ions. Multiple structures form in the presence of potassium and ammonium ions, which is in contrast to the parent oligonucleotide with dT4 loop. 15N-filtered 1H NMR spectra demonstrate that all studied G-quadruplexes exhibit three 15NH4(+) ion binding sites. Topology of intermolecular G-quadruplexes was evaluated by NMR measurements and diffusion experiments. The spherical, prolate-ellipsoid and symmetric cylinder models were used to interpret experimental translational diffusion constants in terms of diameters and lengths of unfolded oligonucleotides and their respective G-quadruplexes. UV melting and annealing curves show that oligonucleotides with non-nucleosidic loop residues fold faster, exhibit no hysteresis, and are less stable than dimeric d(G4T4G4)2 which can be attributed to the absence of H-bonds, stacking between loop residues and the outer G-quartets as well as cation-pi interactions. Oligonucleotide consisting of hexaethylene glycol linkage with only two phosphate groups in the loop exhibits higher melting temperature and more negative deltaH(o) and deltaG(o) values than oligonucleotides with four 1',2'-dideoxyribose or propanediol residues.

DNA↗
PubMedDate not supplied

Comparative fatty acid selectivity of lipases in esterification reactions with glycerol and diol analogues in organic media.

Reaction selectivity of Pseudomonas cepacia, Rhizomucor miehei, and Candida antarctica B lipases was assessed in multicompetitive esterification reaction mixtures containing an homologous series of n-chain even carbon number fatty acid (FA; C4-C18) substrates and a single alcohol cosubstrate (glycerol, 1,2-propanediol (1,2-PD), or 1, 3-propanediol (1,3-PD)) in tert-butyl methyl ether at water activity of 0.69 or 0.90 and a reaction temperature of 35 degrees C. For P. cepacia lipase, the ordinal patterns of FA selectivities observed were, with glycerol, C8 > C10, C6, C16 > other FA; with 1,2-PD and 1, 3-PD, C16 > C8 > C14 > other FA. For R. miehei lipase, the ordinal patterns of FA selectivities observed were, with glycerol, C8 > C12 > C10, C14 > other FA; with 1,2-PD and 1,3-PD, C8 > C12 > other FA. For C. antarctica B lipase, the ordinal patterns of FA selectivities observed were, with glycerol, C8 > C10, C6, C12 > other FA; with 1, 2-PD, C8 > C10, C6 > other FA; and with 1,3-PD, C8 > C10 > C6 > other FA. The differences in selectivity among FA ranged up to 16-fold, depending upon the lipase and alcohol cosubstrate used. These findings represent intrinsic and substrate-modulated features of FA selectivities that are of particular relevance to the use of lipases for acylglycerol synthesis reactions.

Burkholderia cepacia↗
PubMed2000

Selectivity of celite-immobilized patatin (lipid acyl hydrolase) from potato (Solanum tuberosum L.) tubers in esterification reactions As influenced by water activity and glycerol analogues as alcohol acceptors.

Lipid acyl hydrolase (LAH; patatin) was purified from potato tubers by ammonium sulfate fractionation followed by anion-exchange and affinity chromatography. The major protein band of 40-43 kDa on SDS-PAGE appeared to be patatin, and it stained positive for lipase activity on native PAGE. Selectivity of a Celite-immobilized potato LAH in esterification reactions with n-acyl fatty acids (FA; C4, C6, C8, C10, C12, C14, C16, and C18) and alcohol acceptors (n-propanol, 2-propanol, 1,3-propanediol, and glycerol; 1,2-propanediol was not sufficiently reactive) was studied in isooctane. Immobilized LAH was highly selective for medium chain FAs (C8/C10) with a secondary optimum for chain lengths of C14/16. Water activity (a(w)) influenced activity and FA selectivity of the enzyme. Initial rates of ester synthesis were greatest at a(w) of 0.90 for all alcohol acceptors except for glycerol, where greatest initial rates were observed at a(w) of 0.19. Immobilized LAH preparations exhibited a bell-shape pH profile with optimum activity at pH 6-7 for ester synthesis, and no effect of pH on FA selectivity was observed.

Alcohols↗
PubMed1990

(1-Pyrenylmethyl)amino alcohols, a new class of antitumor DNA intercalators. Discovery and initial amine side chain structure-activity studies.

In the series of 1-pyrenylmethylamines studied in this work the relationships among structure, interaction with DNA, and murine antitumor activity were examined. Binding studies show that all of these 1-pyrenylmethylamine derivatives bind to some extent to DNA by intercalation. The presence of additional basic amine groups in the side chain enhances DNA binding due to electrostatic interactions. Those compounds containing only a single basic benzylic amine bind similarly to DNA. Only the presence of bulky side chains appears to decrease the DNA interactions in the compounds examined. Although antitumor activity is seen for (1-pyrenylmethyl)amino alcohols, useful antitumor activity in the series is limited to those congeners bearing the 2-amino-1,3-propanediol-type side chain. These derivatives bind moderately to DNA. DNA binding is a necessary but not sufficient criterion for antitumor activity in the series. In addition, the strength of DNA binding does not correlate with the antitumor activity in the group of active compounds. Three related 2-[(arylmethyl)amino]-1,3-propanediol derivatives (AMAPs) [crisnatol (770U82), 773U82, and 502U83] are currently in clinical trials as potential antitumor agents.

Amino Alcohols↗
PubMed2006

Synthesis and structure-activity relationship effects on the tumor avidity of radioiodinated phospholipid ether analogues.

Radioiodinated phospholipid ether analogues have shown a remarkable ability to selectively accumulate in a variety of human and animal tumors in xenograft and spontaneous tumor rodent models. It is believed that this tumor avidity arises as a consequence of metabolic differences between tumor and corresponding normal tissues. The results of this study indicate that one factor in the tumor retention of these compounds in tumors is the length of the alkyl chain that determines their hydrophobic properties. Decreasing the chain length from C12 to C7 resulted in little or no tumor accumulation and rapid clearance of the compound in tumor-bearing rats within 24 h of administration. Increasing the chain length had the opposite effect, with the C15 and C18 analogues displaying delayed plasma clearance and enhanced tumor uptake and retention in tumor-bearing rats. Tumor uptake displayed by propanediol analogues NM-412 and NM-413 was accompanied by high levels of liver and abdominal radioactivity 24 h postinjection to tumor-bearing rats. Addition of a 2-O-methyl moiety to the propanediol backbone also retarded tumor uptake significantly. A direct comparison between NM-404 and its predecessor, NM-324, in human PC-3 tumor bearing immune-compromised mice revealed a dramatic enhancement in both tumor uptake and total body elimination of NM-404 relative to NM-324. On the basis of imaging and tissue distribution studies in several rodent tumor models, the C18 analogue, NM-404, was chosen for follow-up evaluation in human lung cancer patients. Preliminary results have been extremely promising in that selective uptake and retention of the agent in tumors is accompanied by rapid clearance of background radioactivity from normal tissues, especially those in the abdomen. These results strongly suggest that extension of the human trials to include other cancers is warranted, especially when NM-404 is radiolabeled with iodine-124, a new commercially available positron-emitting isotope. The relatively long physical half-life of 4 days afforded by this isotope appears well-suited to the pharmacodynamic profile of NM-404.

Animals↗
PubMed2006

A one-pot preparation of 1,3-disubstituted azetidines.

A straightforward synthesis of 1,3-disubstituted azetidines has been accomplished via the alkylation of a primary amine with the bis-triflate of a 2-substituted-1,3-propanediol species. This transformation is carried out in one reaction vessel, and elimination of the alkylating reagent is generally not a major byproduct. The scope of this methodology has been investigated using a variety 2-substituted-1,3-propanediols and amine nucleophiles.

Alkylation↗
PubMed2000

Spontaneous hydrolysis reactions of cis- and trans-beta-methyl-4-methoxystyrene oxides (Anethole oxides): buildup of trans-anethole oxide as an intermediate in the spontaneous reaction of cis-anethole oxide.

Rates and products of the reactions of trans- and cis-beta-methyl-4-methoxystyrene oxides (1 and 2) (anethole oxides) and beta,beta-dimethyl-4-methoxystyrene oxide (3) in water solutions in the pH range 4-12 have been determined. In the pH range ca. 8-12, each of these epoxides reacts by a spontaneous reaction. The spontaneous reaction of trans-anethole oxide (1) yields ca. 40% of (4-methoxyphenyl)acetone and 60% of 1-(4-methoxyphenyl)-1, 2-propanediols (erythro:threo ratio ca. 3:1). The spontaneous reaction of cis-anethole oxide is more complicated. The yields of diol and ketone products vary with pH in the pH range 8-11, even though there is not a corresponding change in rate. These results are interpreted by a mechanism in which 2 undergoes isomerization in part to the more reactive trans-anethole oxide (1), which subsequently reacts by acid-catalyzed and/or spontaneous reactions, depending on the pH, to yield diol and ketone products. The buildup of the intermediate trans-anethole oxide in the spontaneous reaction of cis-anethole oxide was detected by (1)H NMR analysis of the reaction mixture. Other primary products of the spontaneous reaction of 2 are (4-methoxyphenyl)acetone (73%) and threo-1-(4-methoxyphenyl)-1,2-propanediol (ca. 3%). The rates and products of the spontaneous reaction of 2 and its beta-deuterium-labeled derivative were determined, and the lack of significant kinetic and partitioning deuterium isotope effects indicates that the isomerization of 2 to ketone and to trans-anethole oxide must occur primarily by nonintersecting reaction pathways.

Anisoles↗
PubMed2006

A new force field (ECEPP-05) for peptides, proteins, and organic molecules.

Parametrization and testing of a new all-atom force field for organic molecules and peptides with fixed bond lengths and bond angles are described. The van der Waals parameters for both the organic molecules and the peptides were taken from J. Phys. Chem. B 2003, 107, 7143 and J. Phys. Chem. B 2004, 108, 12181. First, the values of the 1-4 nonbonded and electrostatic scale factors appropriate to the new force field were determined by computing the conformational energies of six model molecules, namely, ethanol, ethylamine, propanol, propylamine, 1,2-ethanediol, and 1,3-propanediol with different values of these factors. The partial atomic charges of these molecules were obtained by fitting to the electrostatic potentials calculated with the HF/6-31G quantum-mechanical method. Two different charge models (single- and multiple-conformation-derived) were also considered. We demonstrated that the charge model has a stronger effect on the conformational energies than the 1-4 scaling. The choice of a charge model affected the conformational energies of even the smallest molecules considered, whereas the effect of the 1-4 electrostatic or nonbonded scaling was apparent only for 1,3-propanediol. The best agreement with high-level ab initio data was obtained with the multiple-conformation-derived charges and with no scaling of the 1-4 nonbonded or electrostatic interactions (scale factors of 1.0). Next, the torsional parameters of a large number of neutral and charged organic molecules, assumed to be models of the side chains of the 20 naturally occurring amino acids, were computed by fitting to rotational energy profiles obtained from ab initio MP2/6-31G calculations. The quality of the fits was high with average errors for torsional profiles of less than 0.2 kcal/mol. To derive the torsional parameters for the peptide backbone, the partial atomic charges of the 20 neutral and charged amino acids were obtained by fitting to the electrostatic potentials of terminally blocked amino acids using the HF/6-31G quantum-mechanical method. Then, the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe were computed using MP2/6-31G//HF/6-31G quantum-mechanical methods. The phi-psi energy map of Ac-Ala-NMe was used for refinement of the nonbonded parameters for the backbone nitrogen and hydrogen bonded to it. Subsequently, the main-chain torsional parameters were obtained by fitting the molecular mechanics energies to the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe. The transferability of the entire force field was demonstrated by reproducing the main energy minima of terminally blocked Ala3 from the literature. The performance of the force field was also evaluated by simulating crystal structures of small peptides. By comparison of simulated and experimental data, examination of the torsional-angle and atom-positional root-mean-square deviations of the energy-minimized crystal structures from the corresponding X-ray model structures demonstrated high accuracy of the force field.

Algorithms↗
PubMed2006

Influence of intramolecular hydrogen bond strength on OH-stretching overtones.

Vapor-phase OH-stretching overtone spectra of 1,3-propanediol and 1,4-butanediol were recorded and compared to the spectra of ethylene glycol to investigate the effect of increased intramolecular hydrogen bond strength on OH-stretching overtone transitions. The spectra were recorded with laser photoacoustic spectroscopy in the second and third OH-stretching overtone regions. The room-temperature spectra of each molecule are dominated by two conformers that show intramolecular hydrogen bonding. Anharmonic oscillator local-mode calculations of the OH-stretching transitions have been performed to aid assignment of the different conformers in the spectra and to illustrate the effect of the intramolecular hydrogen bonding. The hydrogen bond strength increases in the order ethylene glycol, 1,3-propanediol, and 1,4-butanediol. The overtone transitions of the hydrogen-bonded hydroxyl groups are more difficult to observe with increasing intramolecular hydrogen bond strength. We suggest that the bandwidth of these transitions increases with increasing hydrogen bond strength and with increasing overtone and furthermore that these changes are in part responsible for the lack of observed overtone spectra for complexes.

Butylene Glycols↗