Exploring helix structures of γ-peptides based on 2-(aminomethyl)cyclopentanecarboxylic acid.

Conformational search and density functional theory calculations were performed to explore the preferences of helical structures for chiro-specific oligo-γ-peptides of 2-(aminomethyl)cyclopentanecarboxylic acid (γAmc5) with a cyclopentyl constraint on the Cα-Cß bond in solution. The dimer and tetramer of γAmc5 (1) with homochiral (1S, 2S) configurations exhibited a strong preference for the 9-membered helix foldamer in solution, except for the tetramer in water. However, the oligomers of γAmc5 (1) longer than tetramer preferentially adopted a right-handed (P)-2.614-helix (H1-14) as the peptide sequence becomes longer and as solvent polarity increases. The high stabilities for H1-14 foldamers of γAmc5 (1) in solution were ascribed to the favored solvation free energies. The calculated mean backbone torsion angles for H1-14 helix foldamers of γAmc5 (1) were similar to those calculated for oligomers of other γ-residues with cyclopentane or cyclohexane rings. However, the substitution of cyclopentane constraints on the Cα-Cß bond of the γAmc5 (1) residue resulted in different conformational preferences and/or handedness of helix foldamers. In particular, the pyrrolidine-substituted analogs of the H1-14 foldamers of γAmc5 (1) with adjacent amine diads substituted at a proximal distance are expected to be potential catalysts for the crossed aldol condensation in nonpolar and polar solvents.

Impact of aza-substitutions on the preference of helix handedness for ß-peptide oligomers: a DFT study.

We studied the helix preference of the heterochiral pentamers of cis-2-aminocyclohexanecarboxylic acid (c-ACHC) and cis-2-aminocyclopentanecarboxylic acid (c-ACPC) with alternating backbone configurations by replacing Cß-aza- or Cα-aza-peptide residues using DFT methods in solution. The helix-handedness preferences of two pentamers were strongly affected by the replacement positions (i.e., chiralities) but not depending on the solvent polarity.

Exploring Conformational Preferences of Leu-enkephalin Using the Conformational Search and Double-Hybrid DFT Energy Calculations.

The conformational preferences of Leu-enkephalin (Leu-Enk) were explored by the conformational search and density functional theory (DFT) calculations. By a combination of low-energy conformers of each residue, the initial structures of the neutral Leu-Enk were generated and optimized using the ECEPP3 force field in the gas phase. These structures were reoptimized at the HF/3-21G(d) and M06-2X levels of theory with 6-31G(d) and 6-31+G(d) basis functions. We finally located the 139 structures with the relative energy <10 kcal mol-1 in the gas phase, from which the structures of the corresponding zwitterionic Leu-Enk were generated and reoptimized at the M06-2X/6-31+G(d) level of theory using the implicit solvation model based on density (SMD) in water. The conformational preferences of Leu-Enk were analyzed using Gibbs free energies corrected by single-point energies calculated at the double-hybrid DSD-PBEP86-D3BJ/def2-TZVP level of theory in the gas phase and in water. The neutral Leu-Enk dominantly adopted a folded structure in the gas phase stabilized by three H-bonds with a ßII'-bend-like motif at the Gly3-Phe4 sequence and a close contact between the side chains of Phe4 and Leu5. The zwitterionic Leu-Enk exhibited a folded structure in water stabilized by three H-bonds with double ß-bends such as a ßII' bend at the Gly2-Gly3 sequence and a ßI bend at the Gly3-Phe4 sequence. The calculated ensemble-averaged distance between CGly2 α and CLeu5 α of the zwitterionic Leu-Enk in water is consistent with the value estimated from the simulated annealing using the distance constraints derived from nuclear Overhauser effect spectroscopy (NOESY) spectra in water. Interestingly, the preferred conformations of the neutral and zwitterionic Leu-Enk are new folded structures not predicted by earlier computational studies. According to the refined model of the zwitterionic Leu-Enk bound to δ-opioid receptor (δOR), there were favorable interactions of the terminal charged groups of Leu-Enk with the side chains of charged residues of δOR as well as a favorable CAryl···H interaction of the Phe4 residue of Leu-Enk with Trp284 of δOR. Hence, these favorable interactions would induce the folded structure of the zwitterionic Leu-Enk with double ß-bends isolated in water into the "bioactive conformation" like an extended structure when binding to δOR.

Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study.

Invited for this month's cover picture is the group of Young Kee Kang at Chungbuk National University (Republic of Korea). The cover picture shows the preferred conformation of the hexamer of ϵ-amino acid Amc5 a with a cyclopentane substituent in the backbone investigated using DFT methods in chloroform and water. The Amc5 a hexamer adopted a stable left-handed conformation with a rise of 4.8 Šper turn both in chloroform and water. However, the hexamer of Ampa (an analogue of Amc5 a with replacing cyclopentane by pyrrolidine) adopted different conformations in chloroform and in water. Read the full text of their Research Article at 10.1002/open.202100253.

Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study.

The conformational preferences of oligopeptides of an ϵ-amino acid (2-((1R,3S)-3-(aminomethyl)cyclopentyl)acetic acid, Amc5 a) with a cyclopentane substituent in the Cß -Cγ -Cδ sequence of the backbone were investigated using DFT methods in chloroform and water. The most preferred conformation of Amc5 a oligomers (dimer to hexamer) was the H16  helical structure both in chloroform and water. Four residues were found to be sufficient to induce a substantial H16 helix population in solution. The Amc5 a hexamer adopted a stable left-handed (M)-2.316 helical conformation with a rise of 4.8 Šper turn. The hexamer of Ampa (an analogue of Amc5 a with replacing cyclopentane by pyrrolidine) adopted the right-handed mixed (P)-2.918/16 helical conformation in chloroform and the (M)-2.416 helical conformation in water. Therefore, hexamers of ϵ-amino acid residues exhibited different preferences of helical structures depending on the substituents in peptide backbone and the solvent polarity as well as the chain length.

Conformational Preferences of Cyclopentane-Based Oligo-δ-peptides in the Gas Phase and in Solution.

The conformational preferences of oligomers of δ-amino acid (δAc5 a) with a cyclopentyl constraint in the Cß -Cγ bond of the backbone were investigated by using DFT methods in the gas phase and in solution. The folded structures with C10 H-bonded pseudocycles were most preferred for dimer and tetramer of δAc5 a residues both in chloroform and water. However, for the hexameric Ac-(δAc5 a)6 -NHMe, the mixed H16/14 helical structure was found to be most preferred in chloroform (populated at 68 %), whereas the H14 helical structure was the most dominant conformation in water (populated at 60 %). The stability of the former was ascribed to the intrinsic conformational energy, whereas the solvation free energy was crucial to stabilize the latter. Pyrrolidine-substituted analogues of the hexameric Ac-(δAc5 a)6 -NHMe, with adjacent amine diads that are almost exactly one turn apart with two nitrogen atoms separated by ca. 5.5 Å, adopted helical structures. They are potential catalysts in nonpolar and polar solvents as they have similar structures to a helical 1 : 2 α:ß-heptapeptide that exhibited good catalytic performance in the crossed aldol condensation.

Impact of the COVID-19 pandemic on women's health nursing clinical practicums in the spring 2020 semester in Korea: a nationwide survey study.

Purpose: This study investigated the impact of coronavirus disease 2019 (COVID-19) on women's health nursing clinical practicums in undergraduate nursing schools in Korea during the spring 2020 semester. Methods: A cross-sectional online survey on clinical practicum teaching experiences in the spring 2020 semester was distributed to members of the Korean Society of Women Health Nursing (KSWHN) who taught undergraduate nursing. One faculty member from each of 203 institutions was requested to respond and there were no duplicate participants. Seventy-nine participants (38.9%) responded and 74 responses were analyzed. Descriptive statistics were presented for all survey items. Results: Fifty-two faculty members (70.3%) belonged to universities and 22 (29.7%) taught at colleges. Thirty-eight (51.4%) answered that their institutions had affiliated teaching hospitals. More than half (52.7%) conducted hospital-based clinical practicums either entirely (n=20) or partially (n=19), whereas the rest of them (47.3%) conducted clinical practicums at school or home via online teaching. The typical teaching methods for offline or online education were case conferences, tests or quizzes, scenario studies, nursing skill practicums, (virtual) nursing simulations, and simulated patient education. Most of faculties (93.2%) supported the development of an educational platform to share educational materials and resources, such as case scenarios. Conclusion: Nursing faculty members utilized various teaching methods to enhance clinical skills and mitigate limited clinical exposure during the early stage of the COVID-19 pandemic. The KSWHN should move forward to develop an education platform and modalities for members who face many challenges related to the accessibility and quality of nursing education contents.

Conformational preferences of cationic ß-peptide in water studied by CCSD(T), MP2, and DFT methods.

The conformational preferences of the cationic nylon-3 ßNM [(3R,4)-diaminobutanoic acid, dAba] dipeptide in water were explored as the first step to understand the mode of action of polymers of ßNM against phylogenetically diverse and intrinsically drug-resistant pathogenic fungi. The CCSD(T), MP2, M06-2X, ωB97X-D, B2PLYP-D3BJ, and DSD-PBEP86-D3BJ levels of theory with various basis sets were assessed for relative energies of the 45 local minima of the cationic Ac-dAba-NHMe located at the SMD M06-2X/6-31+G(d) level of theory in water against the benchmark CCSD(T)/CBS-limit energies in water. The best performance was obtained at the double-hybrid DSD-PBEP86-D3BJ/def2-QZVP level of theory with RMSD = 0.12 kcal/mol in water. The M06-2X/def2-QZVP level of theory predicted reasonably the conformational preference with RMSD = 0.38 kcal/mol in water and may be an alternative level of theory with marginal deviations for the calculation of conformational energies of relatively longer cationic peptides in water. In particular, the H 14-helical structures appeared to be the most feasible conformations for the cationic Ac-dAba-NHMe populated at 48-64% by relative free energies in water. The hexamer built from the H 14-structure of the cationic Ac-dAba-NHMe adopted a left-handed 314-helix, which has a slightly narrower radius and a longer rise than the regular 314-helix of ß-peptides. Hence, the 314-helices of oligomers or polymers of the cationic dAba residues are expected to be the active conformation to exhibit the ability to bridge between charged lipid head groups that might cause a local depression or invagination of the membrane of fungi.

Organocatalytic Asymmetric Addition of Aldehyde to Nitroolefin by H-d-Pro-Pro-Glu-NH2: A Mechanistic Study.

The mechanism of the asymmetric addition of aldehyde (butanal) to nitroolefin (ß-nitrostyrene) catalyzed by H-d-Pro-Pro-Glu-NH2 (dPPE-NH2; 1) was explored using density functional theory methods in chloroform. By conformational search, it was confirmed that catalyst 1 and its enamine intermediate adopted a dominant conformation with a ßI structure stabilized by a C10 H-bond between the C=O of d-Pro1 and C-terminal NH2 proton and by an additional H-bond between the side chain and the backbone of Glu3. This ßI turn structure was conserved all along the catalytic cycle. Consistently with the kinetic studies, the C-C bond formation between the enamine and electrophile was also confirmed as the rate-determining step. The stereoselectivity results from a re → re prochiral approach of enamine and ß-nitrostyrene with a gauche- orientation of the double bonds. Although it was suggested as the possible formation of dihydrooxazine oxide species, this process was confirmed to be kinetically less accessible than the formation of acyclic nitronate. In particular, our calculated results supported that the carboxylic acid group of Glu3 in 1 played a central role by acting as general acid/base all along the catalytic cycle and orienting the asymmetric C-C bond formation.

Effects of a cultural nursing course to enhance the cultural competence of nursing students in Korea.

PURPOSE: With Korea's recent rapid change into a multicultural society, cultural competence is being emphasized as a core nursing competency. This study investigated the effects of a cultural nursing course that aimed to enhance the cultural competence of nursing students in Korea. METHODS: This was a single-group pre- and post-comparison study. The subjects were 69 nursing students at Dongyang University who attended a cultural nursing course in 2015, of whom 62 students responded to the survey. The 13-week cultural nursing course was held for 2 hours a week. The methods of the course included small group activities, discussions and presentations, experiential learning, reflective activities, and lectures. Nursing students' cultural competence was measured pre- and post-course with the Cultural Competence Scale for Korean Nurses, which contains 33 items scored on a 7-point Likert scale. RESULTS: After completing the cultural nursing course, students' total cultural competence scores increased, as did their scores in each category (cultural awareness, cultural knowledge, cultural sensitivity, and cultural skills) (P<0.001). There was no significant difference in cultural competence by gender (P<0.001). CONCLUSION: This cultural nursing course was found to be effective in enhancing the cultural competence of nursing students. Therefore, the educational program developed in this study can be extended to other university-level nursing programs in Korea.

Item development process and analysis of 50 case-based items for implementation on the Korean Nursing Licensing Examination.

PURPOSE: The purpose of this study was to improve the quality of items on the Korean Nursing Licensing Examination by developing and evaluating case-based items that reflect integrated nursing knowledge. METHODS: We conducted a cross-sectional observational study to develop new case-based items. The methods for developing test items included expert workshops, brainstorming, and verification of content validity. After a mock examination of undergraduate nursing students using the newly developed case-based items, we evaluated the appropriateness of the items through classical test theory and item response theory. RESULTS: A total of 50 case-based items were developed for the mock examination, and content validity was evaluated. The question items integrated 34 discrete elements of integrated nursing knowledge. The mock examination was taken by 741 baccalaureate students in their fourth year of study at 13 universities. Their average score on the mock examination was 57.4, and the examination showed a reliability of 0.40. According to classical test theory, the average level of item difficulty of the items was 57.4% (80%-100% for 12 items; 60%-80% for 13 items; and less than 60% for 25 items). The mean discrimination index was 0.19, and was above 0.30 for 11 items and 0.20 to 0.29 for 15 items. According to item response theory, the item discrimination parameter (in the logistic model) was none for 10 items (0.00), very low for 20 items (0.01 to 0.34), low for 12 items (0.35 to 0.64), moderate for 6 items (0.65 to 1.34), high for 1 item (1.35 to 1.69), and very high for 1 item (above 1.70). The item difficulty was very easy for 24 items (below -2.0), easy for 8 items (-2.0 to -0.5), medium for 6 items (-0.5 to 0.5), hard for 3 items (0.5 to 2.0), and very hard for 9 items (2.0 or above). The goodness-of-fit test in terms of the 2-parameter item response model between the range of 2.0 to 0.5 revealed that 12 items had an ideal correct answer rate. CONCLUSION: We surmised that the low reliability of the mock examination was influenced by the timing of the test for the examinees and the inappropriate difficulty of the items. Our study suggested a methodology for the development of future case-based items for the Korean Nursing Licensing Examination.

Relevance of the test content of the Korean Nursing Licensing Examination to nursing job.

PURPOSE: This study aimed at identifying if there is a relevance of content of the Korean Nursing Licensing Examination (KNLE) revised in 2014 to nursing job. It will be able to provide the validity of revised content of the KNLE. METHODS: From October 13 to November 13, 2015, print version of 8 duties with 49-tasks, 155-job item questionnaires were distributed to 1,305 hospital nurses and 202 nursing faculties in Korea. Results were treated by descriptive statistics and comparison analysis. There were responses from 946 nurses or professors (72.5%). RESULTS: The relevance of test content of KNLE to nursing job was shown to be valid with over 3 points out of 4 point Likert scale in all items: from 3.23 at lowest to 3.64 at top. CONCLUSION: Above results showed that the revised version of KNLE in 2014 was valid to test the nursing students' knowledge for job performance.

The job analysis of Korean nurses as a strategy to improve the Korean Nursing Licensing Examination.

PURPOSE: This study aimed at characterizing Korean nurses' occupational responsibilities to apply the results for improvement of the Korean Nursing Licensing Examination. METHODS: First, the contents of nursing job were defined based on a focus group interview of 15 nurses. Developing a Curriculum (DACOM) method was used to examine those results and produce the questionnaire by 13 experts. After that, the questionnaire survey to 5,065 hospital nurses was done. RESULTS: The occupational responsibilities of nurses were characterized as involving 8 duties, 49 tasks, and 303 task elements. Those 8 duties are nursing management and professional development, safety and infection control, the management of potential risk factors, basic nursing and caring, the maintenance of physiological integrity, medication and parenteral treatments, socio-psychological integrity, and the maintenance and improvement of health. CONCLUSION: The content of Korean Nursing Licensing Examination should be improved based on 8 duties and 49 tasks of the occupational responsibilities of Korean nurses.

Hairpin formation promoted by the heterochiral dinipecotic acid segment: A DFT study.

Conformational preferences for the turn and ß-hairpin structures of Ala-based peptides [Ac-Ala(n)-(R)-Nip-(S)-Nip-Ala(n)-X (n = 0-2; X = NHMe or NMe2)] containing nipecotic acid (Nip) residues were carried out using the density functional M06-2X and the implicit solvation model SMD in CH2Cl2 and/or water. The turn structure of the (R)-Nip-(S)-Nip segment with a C10 H-bond between two terminal groups was found to be most preferred (populated at 98.9%) in CH2Cl2; this structure is consistent with IR and (1)H NMR results. The stabilities of the ß-hairpins containing the (R)-Nip-(S)-Nip segment as a turn motif relative to the extended structures increased with peptide sequence length. The relative strengths of the H-bonds between the carbonyl oxygen and the amide hydrogen appeared to be responsible for stabilizing the turn and ß-hairpin structures in CH2Cl2. In addition, the (R)-Nip-(S)-Nip segment exhibited the capability to be incorporated into one of the two ß-turn motifs of gramicidin S (GS). The structure of this GS derivative (GS-Nip2 ) was generally similar to the native peptide but was less hydrophobic and it is therefore expected to exhibit lower hemolytic activity; however, further experiments are needed to evaluate its antimicrobial activity. The structure of GS-Nip2 was somewhat more flexible than GS in solvents of higher polarity. Thus, our calculated results regarding the turn and ß-hairpin motifs of the (R)-Nip-(S)-Nip segment indicate that this structure might be useful for the design of bioactive macrocyclic peptides containing ß-hairpin mimics as well as binding epitopes in protein-protein and protein-nucleic acid recognitions.

Sex differences in the relation of body composition to cardiovascular parameters and functions in Korean adolescents: a school-based study.

OBJECTIVE: Obesity in adolescence is associated with increased cardiovascular risk. The patterns of obesity and body composition differ between boys and girls. It is uncertain how body composition correlates with the cardiovascular system and whether such correlations differ by sex in adolescents. METHODS: Body composition (fat-free mass (FFM), adipose mass, waist circumference (WC)) and cardiovascular parameters and functions were studied in 676 healthy Korean adolescents aged 12-16 years. Partial correlation and path analyses were done. RESULTS: WC correlated with stroke volume (SV) and cardiac output (CO), systolic blood pressure (SBP) and pulse pressure (PP), cardiac diastolic function (ratio of early to late filling velocity (E/A ratio)), and vascular function (pulse wave velocity (PWV)) in boys. Adipose mass was related to SV, CO, SBP, PP, left ventricular mass (LVM), and PWV in girls - and to E/A ratio in both sexes. FFM affected SV, CO, SBP, and PP in both sexes and LVM in boys. Cardiac systolic functions had no relation with any body composition variable in either sex. CONCLUSION: In adolescence, the interdependence of the cardiovascular system and the body composition differs between sexes. Understanding of those relations is required to control adolescent obesity and prevent adult cardiovascular disease.

Conformational preferences of 4-chloroproline residues.

Conformational preferences of the (2S,4R)-4-chloroproline (Clp) and (2S,4S)-4-chloroproline (clp) residues are explored at the M06-2X/cc-pVTZ//M06-2X/6-31+G(d) level of theory in the gas phase and in water, where solvation free energies were calculated using the implicit solvation model, and by an X-ray diffraction study in the solid state. In the gas phase, the down-puckered γ-turn structure with the trans prolyl peptide bond is most preferred for both Ac-Clp-NHMe and Ac-clp-NHMe, in which the C(7) hydrogen bond between two terminal groups seems to play a role, as found for Ac-Pro-NHMe. In water, the Clp residue has a strong preference for the up-puckered PP(II) structure, whereas the up-puckered PP(II) structure prevails a little over the down-puckered PP(II) structure for the clp residue, similar to the Pro residue. Hence, our calculated results on the puckering preference of the Clp and clp residues in water are in accord with the observed results deduced from the relative stabilities of the triple helices of the collagen model peptides. The X-ray structure of Ac-clp-NHMe was found to be the most preferred in water but that of Ac-Clp-NHMe was located as a local minimum with ΔG = 2.0 kcal/mol. In particular, the X-ray structure of Ac-Clp-NHMe was quite different from that of Ac-Clp-OMe but similar to that of Ac-Pro-NHMe. The lowest rotational barriers to the prolyl cis-trans isomerization for Ac-Clp-NHMe become nearly the same as those for Ac-Pro-NHMe in water, whereas the barriers are lower by ∼2 kcal/mol for Ac-clp-NHMe. It was found that the cis-trans isomerization may proceed through the clockwise or anticlockwise rotations for Ac-Clp-NHMe and the anticlockwise rotation for Ac-clp-NHMe and Ac-Pro-NHMe in water.

Conformational preference and cis-trans isomerization of 4-methylproline residues.

Conformational preferences and prolyl cis-trans isomerizations of the (2S,4S)-4-methylproline (4S-MePro) and (2S,4R)-4-methylproline (4R-MePro) residues are explored at the M06-2X/cc-pVTZ//M06-2X/6-31+G(d) level of theory in the gas phase and in water, where solvation free energies were calculated using the implicit SMD model. In the gas phase, the down-puckered γ-turn structure with the trans prolyl peptide bond is most preferred for both Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe, in which the C(7) hydrogen bond between two terminal groups seems to play a role, as found for Ac-Pro-NHMe. Because of the C(7) hydrogen bonds weakened by the favorable direct interactions between the backbone C==O and H--N groups and water molecules, the 4S-MePro residue has a strong preference of the up-puckered polyproline II (PP(II)) structure over the down-puckered PP(II) structure in water, whereas the latter somewhat prevails over the former for the 4R-MePro residue. However, these two structures are nearly equally populated for Ac-Pro-NHMe. The calculated populations for the backbone structures of Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe in water are reasonably consistent with CD and NMR experiments. In particular, our calculated results on the puckering preference of the 4S-MePro and 4R-MePro residues with the PP(II) structures are in accord with the observed results for the stability of the (X-Y-Gly)(7) triple helix with X = 4R-MePro or Pro and Y = 4S-MePro or Pro. The calculated rotational barriers indicate that the cis-trans isomerization may in common proceed through the anticlockwise rotation for Ac-4S-MePro-NHMe, Ac-4R-MePro-NHMe, and Ac-Pro-NHMe in water. The lowest rotational barriers become higher by 0.24-1.43 kcal/mol for Ac-4S-MePro-NHMe and Ac-4R-MePro-NHMe than those for Ac-Pro-NHMe in water.

Conformational preferences and cis-trans isomerization of L-3,4-dehydroproline residue.

The conformational study of N-acetyl-N'-methylamide of L-3,4-dehydroproline (Ac-Dhp-NHMe, the Dhp dipeptide) is carried out using hybrid density functional methods with the self-consistent reaction field method in the gas phase and in solution (chloroform and water). The incorporation of a double bond between C(beta) and C(gamma) into the prolyl ring results in the puckering, backbone population, and barriers to prolyl cis-trans isomerization different from those of the Pro dipeptide. For local minima of the Dhp dipeptide in the gas phase and in water, the C(beta)-C(gamma) bonds become shorter by approximately 0.2 A and the bond angles C(alpha)-C(beta)-C(gamma) and C(beta)-C(gamma)-C(delta) are widened by approximately 8 degrees than those of the Pro dipeptide, and the puckering amplitude is computed to be 0.01-0.07 A, indicating that the 3,4-dehydroprolyl ring is quite less puckered. However, polyproline-like conformations become preferred and the relative stability of the conformation tC with a C(7) intramolecular hydrogen bond decreases as the solvent polarity increases, as found for the Pro dipeptide. The barriers to cis-trans isomerization of the Ac-Dhp peptide bond increase with the increase of solvent polarity and the isomerization is likely to proceed through the clockwise rotation in water, as found for the prolyl peptide bond. The hydrogen bond between the prolyl nitrogen and the following amide N-H group seems to contribute in stabilizing the transition state structures.

Puckering transitions of pseudoproline residues.

The puckering transitions of pesudoprolines such as oxazolidine and thiazolidine residues (Oxa and Thz dipeptides) with trans and cis prolyl peptide bonds were explored by optimizations along the endocyclic torsion angle chi(1) using quantum-chemical methods in the gas phase and in water. The overall shapes of the potential energy surfaces for Oxa and Thz dipeptides in the gas phase and in water are similar to those for the Pro dipeptide, although there are some differences in relative stabilities of local minima and in barriers to puckering transition. On the whole, the barriers to puckering transition for Oxa and Thz dipeptides are computed to be 0.8-3.2 kcal/mol at the B3LYP/6-311++G(d,p) level in the gas phase and in water, which are lower by 0.5-1.9 kcal/mol than those for the Pro dipeptide. The n --> sigma* interactions for the delocalization of the lone pair of the prolyl amide nitrogen into the antibonding orbitals that are anti to the lone pair appear to play a role in stabilizing the nonplanar puckered transition states over the corresponding planar structures. The calculated barriers indicate that the down-to-up puckering transition can proceed in the orders Pro < Oxa < Thz in the gas phase and Pro approximately Oxa < Thz in water. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 444-455, 2009.

Conformational preferences of pseudoproline residues.

The conformational study on N-acetyl-N'-methylamides of oxazolidine and thiazolidine residues (Ac-Oxa-NHMe and Ac-Thz-NHMe) is carried out using ab initio HF and density functional B3LYP methods with the self-consistent reaction field method to explore the effects of the replacement of the C(gamma)H(2) group in the prolyl ring by oxygen or sulfur atoms on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). As the solvent polarity increases, the conformations C with the C7 intramolecular hydrogen bonds become depopulated, the PPII- or PPI-like conformations F become more populated, and the cis populations increase for both Oxa and Thz dipeptides, as found for the Pro dipeptide, although the populations of backbone conformations and puckerings are different in pseudoproline and proline dipeptides. As the increase of solvent polarity, the populations of the trans/up conformations decrease for Oxa and Thz dipeptides, but they increase for the Pro dipeptide. It is found that the cis-trans isomerization proceeds through the anticlockwise rotation with omega' approximately -60 degrees about the oxazolidyl peptide bond and the clockwise rotation with omega' approximately +120 degrees about the thiazolidyl peptide bond in the gas phase and in solution, whereas the clockwise rotation is preferred for the prolyl peptide bond. The pertinent distance d(N...H-N(NHMe)) and the pyramidality of the prolyl nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure but the lower rotational barriers for Oxa and Thz dipeptides than those for the Pro dipeptide, which is observed from experiments, cannot be rationalized. The calculated cis populations and rotational barriers to the cis-trans isomerization for both Oxa and Thz dipeptides in chloroform and/or water are consistent with the experimental values.