PeerJ physical chemistry最新文献_第3页

UV synchrotron radiation linear dichroism spectroscopy of the anti-psoriatic drug anthralin 抗银屑病药物蒽林的紫外同步辐射线性二色光谱

PeerJ physical chemistry Pub Date : 2019-11-15 DOI: 10.7717/peerj-pchem.5

D. D. Nguyen, D. D. Nguyen, N. Jones, S. Hoffmann, J. Spanget-Larsen

引用次数: 3

Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations 广义系综分子动力学模拟中平行运行数和偏强替换频率的影响

PeerJ physical chemistry Pub Date : 2019-10-15 DOI: 10.7717/peerj-pchem.4

Takuya Shimato, K. Kasahara, J. Higo, Takuya Takahashi

引用次数: 3

Structure and diffusion of molten alkali carbonate salts at the liquid-vacuum interface 熔融碳酸碱盐在液-真空界面处的结构和扩散

PeerJ physical chemistry Pub Date : 2019-10-15 DOI: 10.7717/peerj-pchem.3

G. Lindberg

引用次数: 0

Outline of an experimental design aimed to detect a protein A mirror image in solution. 一个旨在检测溶液中蛋白质镜像的实验设计大纲。

PeerJ physical chemistry Pub Date : 2019-10-15 DOI: 10.7717/peerj-pchem.2

Osvaldo A Martin, Yury Vorobjev, Harold A Scheraga, Jorge A Vila

{"title":"Outline of an experimental design aimed to detect a protein A mirror image in solution.","authors":"Osvaldo A Martin, Yury Vorobjev, Harold A Scheraga, Jorge A Vila","doi":"10.7717/peerj-pchem.2","DOIUrl":"https://doi.org/10.7717/peerj-pchem.2","url":null,"abstract":"There is abundant theoretical evidence indicating that a mirror image of Protein A may occur during the protein folding process. However, as to whether such mirror image exists in solution is an unsolved issue. Here we provide outline of an experimental design aimed to detect the mirror image of Protein A in solution. The proposal is based on computational simulations indicating that the use of a mutant of protein A, namely Q10H, could be used to detect the mirror image conformation in solution. Our results indicate that the native conformation of the protein A should have a pKa, for the Q10H mutant, at ≈6.2, while the mirror-image conformation should have a pKa close to ≈7.3. Naturally, if all the population is in the native state for the Q10H mutant, the pKa should be ≈6.2, while, if all are in the mirror-image state, it would be ≈7.3, and, if it is a mixture, the pKa should be largerthan 6.2, presumably in proportion to the mirror population. In addition, evidence is provided indicating the tautomeric distribution of H10 must also change between the native and mirror conformations. Although this may not be completely relevant for the purpose of determining whether the protein A mirror image exists in solution, it could provide valuable information to validate the pKa findings. We hope this proposal will foster experimental work on this problem either by direct application of our proposed experimental design or serving as inspiration and motivation for other experiments.","PeriodicalId":93220,"journal":{"name":"PeerJ physical chemistry","volume":"1 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168520/pdf/nihms-1572619.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39071443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Effect of femtosecond laser pulse repetition rate on nonlinear optical properties of organic liquids 飞秒激光脉冲重复频率对有机液体非线性光学性质的影响

PeerJ physical chemistry Pub Date : 2019-10-15 DOI: 10.7717/peerj-pchem.1

S. Maurya, D. Yadav, D. Goswami

引用次数: 9

Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities HIV-1整合酶抑制剂与病毒DNA末端结合的光谱和计算研究

PeerJ physical chemistry Pub Date : 2019-07-01 DOI: 10.7717/PEERJ-PCHEM.6

Léa El Khoury, Krystel El Hage, Jean‐Philip Piquemal, S. Fermandjian, R. Maroun, N. Gresh, Zeina Hobaika

{"title":"Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities","authors":"Léa El Khoury, Krystel El Hage, Jean‐Philip Piquemal, S. Fermandjian, R. Maroun, N. Gresh, Zeina Hobaika","doi":"10.7717/PEERJ-PCHEM.6","DOIUrl":"https://doi.org/10.7717/PEERJ-PCHEM.6","url":null,"abstract":"Three integrase strand transfer inhibitors are in intensive clinical use, raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG). The onset of integrase resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviral nucleobases, which are little, if at all, mutation-prone. We report experimental results of anisotropy fluorescence titrations of viral DNA by these three drugs. These show the DTG > EVG > RAL ranking of their inhibitory activities of the intasome to correspond to that of their free energies of binding, ∆Gs, to retroviral DNA, and that such a ranking is only governed by the binding enthalpies, ∆H, the entropy undergoing marginal variations. We sought whether this ranking might be reproduced through quantum chemistry (QC) Density Functional Theory calculations of intermolecular interaction energies between simplified models consisting of sole halobenzene ring and the highly conserved retroviral nucleobases G4 and C16. These calculations showed that binding of EVG has a small preference over DTG, while RAL ranked third. This indicates that additional interactions of the diketoacid parts of the drugs with DNA could be necessary to further enable preferential binding of DTG. The corresponding ∆Etotvalues computed with a polarizable molecular mechanics/dynamics procedure, Sum of Interactions Between Fragments Ab initio computed (SIBFA), showed good correlations with this ∆E(QC) ranking. These validations are an important step toward the use of polarizable molecular dynamics simulations on DTG or EVG derivatives in their complexes with the complete intasome, an application now motivated and enabled by the advent of currently developed and improved massively parallel software.","PeriodicalId":93220,"journal":{"name":"PeerJ physical chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49013093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

High throughput virtual screening of 230 billion molecular solar heat battery candidates 2300亿个分子太阳能热电池候选物的高通量虚拟筛选

PeerJ physical chemistry Pub Date : 2019-04-24 DOI: 10.26434/chemrxiv.8003813.v1

Mads Koerstz, Anders S. Christensen, K. Mikkelsen, M. Nielsen, Jan H. Jensen

{"title":"High throughput virtual screening of 230 billion molecular solar heat battery candidates","authors":"Mads Koerstz, Anders S. Christensen, K. Mikkelsen, M. Nielsen, Jan H. Jensen","doi":"10.26434/chemrxiv.8003813.v1","DOIUrl":"https://doi.org/10.26434/chemrxiv.8003813.v1","url":null,"abstract":"The dihydroazulene/vinylheptafulvene (DHA/VHF) thermocouple is a promising candidate for thermal heat batteries that absorb and store solar energy as chemical energy without the need for insulation. However, in order to be viable the energy storage capacity and lifetime of the high energy form (i.e., the free energy barrier to the back reaction) of the canonical parent compound must be increased significantly to be of practical use. We use semiempirical quantum chemical methods, machine learning, and density functional theory to virtually screen over 230 billion substituted DHA molecules to identify promising candidates. We identify a molecule with a predicted energy density of 0.38 kJ/g, which is significantly larger than the 0.14 kJ/g computed for the parent compound. The free energy barrier to the back reaction is 11 kJ/mol higher than the parent compound, which should correspond to a half-life of about 10 days—4 months. This is considerably longer than the 3–39 h (depending on solvent) observed for the parent compound and sufficiently long for many practical applications. Our paper makes two main important contributions: (1) a novel and generally applicable methodological approach that makes screening of huge libraries for properties involving chemical reactivity with modest computational resources, and (2) a clear demonstration that the storage capacity of the DHA/VHF thermocouple cannot be increased to >0.5 kJ/g by combining simple substituents.","PeriodicalId":93220,"journal":{"name":"PeerJ physical chemistry","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47440562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13