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f | 1 | { | f | 1 | { |
2 | "author": "Mast, Thilo", | 2 | "author": "Mast, Thilo", | ||
3 | "author_email": "", | 3 | "author_email": "", | ||
4 | "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700", | 4 | "creator_user_id": "17755db4-395a-4b3b-ac09-e8e3484ca700", | ||
5 | "doi": "10.35097/1132", | 5 | "doi": "10.35097/1132", | ||
6 | "doi_date_published": "2023", | 6 | "doi_date_published": "2023", | ||
7 | "doi_publisher": "", | 7 | "doi_publisher": "", | ||
8 | "doi_status": "True", | 8 | "doi_status": "True", | ||
9 | "groups": [], | 9 | "groups": [], | ||
10 | "id": "b6b394be-ed07-4b3d-b51f-19f700418b5e", | 10 | "id": "b6b394be-ed07-4b3d-b51f-19f700418b5e", | ||
11 | "isopen": false, | 11 | "isopen": false, | ||
12 | "license_id": "CC BY-SA 4.0 Attribution-ShareAlike", | 12 | "license_id": "CC BY-SA 4.0 Attribution-ShareAlike", | ||
13 | "license_title": "CC BY-SA 4.0 Attribution-ShareAlike", | 13 | "license_title": "CC BY-SA 4.0 Attribution-ShareAlike", | ||
14 | "metadata_created": "2023-08-04T08:50:09.045625", | 14 | "metadata_created": "2023-08-04T08:50:09.045625", | ||
t | 15 | "metadata_modified": "2023-08-04T08:50:09.045632", | t | 15 | "metadata_modified": "2023-08-04T08:51:47.100873", |
16 | "name": "rdr-doi-10-35097-1132", | 16 | "name": "rdr-doi-10-35097-1132", | ||
17 | "notes": "Abstract: Die archaeale Protonenpumpe Bacteriorhodopsin | 17 | "notes": "Abstract: Die archaeale Protonenpumpe Bacteriorhodopsin | ||
18 | nutzt Sonnenlicht um einen Protonengradienten \u00fcber der | 18 | nutzt Sonnenlicht um einen Protonengradienten \u00fcber der | ||
19 | Zellmembran aufzubauen. Der Mechanismus der Energieumwandlung basiert | 19 | Zellmembran aufzubauen. Der Mechanismus der Energieumwandlung basiert | ||
20 | auf einem gut erforschten Photozyklus. Obwohl schon \u00fcber 45 Jahre | 20 | auf einem gut erforschten Photozyklus. Obwohl schon \u00fcber 45 Jahre | ||
21 | an diesem bioenergetischen Modellsystem geforscht wurde, sind noch | 21 | an diesem bioenergetischen Modellsystem geforscht wurde, sind noch | ||
22 | immer wenig Informationen \u00fcber den letzten Schritt dieses | 22 | immer wenig Informationen \u00fcber den letzten Schritt dieses | ||
23 | Photozykluses vorhanden: den \u00dcbergang vom O zum Grundzustand | 23 | Photozykluses vorhanden: den \u00dcbergang vom O zum Grundzustand | ||
24 | (bR). Es wird jedoch angenommen, dass ein langreichweitiger | 24 | (bR). Es wird jedoch angenommen, dass ein langreichweitiger | ||
25 | Protonentransfer den bR Zustand wiederherstellt. Diese Arbeit zielt | 25 | Protonentransfer den bR Zustand wiederherstellt. Diese Arbeit zielt | ||
26 | darauf ab, weiteren Aufschluss \u00fcber die mechanistischen Details | 26 | darauf ab, weiteren Aufschluss \u00fcber die mechanistischen Details | ||
27 | und thermodynamischen/kinetischen Eigenschaften des O\u2192bR | 27 | und thermodynamischen/kinetischen Eigenschaften des O\u2192bR | ||
28 | \u00dcbergangs zu geben. Um dies zu bewerkstelligen, wurden | 28 | \u00dcbergangs zu geben. Um dies zu bewerkstelligen, wurden | ||
29 | computergest\u00fctze Rechenmethoden als brauchbare Erg\u00e4nzung zum | 29 | computergest\u00fctze Rechenmethoden als brauchbare Erg\u00e4nzung zum | ||
30 | Experiment verwendet, da die Handhabung von Membranproteinen und die | 30 | Experiment verwendet, da die Handhabung von Membranproteinen und die | ||
31 | gesetzten Ziele f\u00fcr experimentelle Methoden eine schwierige | 31 | gesetzten Ziele f\u00fcr experimentelle Methoden eine schwierige | ||
32 | Aufgabe darstellen. Zun\u00e4chst wurden Strukturmodelle mit Hilfe von | 32 | Aufgabe darstellen. Zun\u00e4chst wurden Strukturmodelle mit Hilfe von | ||
33 | enhanced sampling Methoden f\u00fcr den O, bR und den O* | 33 | enhanced sampling Methoden f\u00fcr den O, bR und den O* | ||
34 | Intermediatszustand erstellt. F\u00fcr die Simulation der | 34 | Intermediatszustand erstellt. F\u00fcr die Simulation der | ||
35 | (langreichweitigen) Protonentransfer- reaktionen wurde ein hybrides | 35 | (langreichweitigen) Protonentransfer- reaktionen wurde ein hybrides | ||
36 | QM/MM Set-up basierend auf der semiempirischen Quantenchemie- Methode | 36 | QM/MM Set-up basierend auf der semiempirischen Quantenchemie- Methode | ||
37 | DFTB3 und dem CHARMM36 Kraftfeld verwendet. Die mit dem | 37 | DFTB3 und dem CHARMM36 Kraftfeld verwendet. Die mit dem | ||
38 | Protonentransfer assoziierte \u00c4nderung der Gibbs\u2019schen Freien | 38 | Protonentransfer assoziierte \u00c4nderung der Gibbs\u2019schen Freien | ||
39 | Energie wurde mit Hilfe von Freie-Energie-Techniken in Kombination mit | 39 | Energie wurde mit Hilfe von Freie-Energie-Techniken in Kombination mit | ||
40 | einer fortgeschrittenen Reaktionskoordinate, die auf der center of | 40 | einer fortgeschrittenen Reaktionskoordinate, die auf der center of | ||
41 | excess charge- Darstellung basiert, aufgekl\u00e4rt. Die Ergebnisse | 41 | excess charge- Darstellung basiert, aufgekl\u00e4rt. Die Ergebnisse | ||
42 | weisen darauf hin, dass es sich bei der O\u2192bR Konversion um einen | 42 | weisen darauf hin, dass es sich bei der O\u2192bR Konversion um einen | ||
43 | leicht exergonen Prozess handelt, in dem der O* Zustand ein | 43 | leicht exergonen Prozess handelt, in dem der O* Zustand ein | ||
44 | metastabiler Zwischenzustand bildet. Bez\u00fcglich des | 44 | metastabiler Zwischenzustand bildet. Bez\u00fcglich des | ||
45 | Protonentransfer-Pfads wurde eine interessante Feststellung gemacht: | 45 | Protonentransfer-Pfads wurde eine interessante Feststellung gemacht: | ||
46 | Der langreichweitige Protonentransfer wird \u00fcber einen | 46 | Der langreichweitige Protonentransfer wird \u00fcber einen | ||
47 | Protonen-Loch-/inversen Grotthuss-Mechanismus vollzogen. Zudem wird | 47 | Protonen-Loch-/inversen Grotthuss-Mechanismus vollzogen. Zudem wird | ||
48 | dieser Ladungstransfer begleitet von der Umorientierung einer | 48 | dieser Ladungstransfer begleitet von der Umorientierung einer | ||
49 | funktionell wichtigen, positiv geladenen Arginin Seitenkette sowie der | 49 | funktionell wichtigen, positiv geladenen Arginin Seitenkette sowie der | ||
50 | Ausbildung der proton release group. Im Zuge dieser Studien, wurde des | 50 | Ausbildung der proton release group. Im Zuge dieser Studien, wurde des | ||
51 | Weiteren die Genauigkeit von DFTB3 f\u00fcr Protonentransferreaktionen | 51 | Weiteren die Genauigkeit von DFTB3 f\u00fcr Protonentransferreaktionen | ||
52 | evaluiert. Die Methode bewies sich als leistungsstark f\u00fcr die | 52 | evaluiert. Die Methode bewies sich als leistungsstark f\u00fcr die | ||
53 | Beschreibung dieser Reaktionen mit einer geringf\u00fcgigen Tendenz | 53 | Beschreibung dieser Reaktionen mit einer geringf\u00fcgigen Tendenz | ||
54 | f\u00fcr die Untersch\u00e4tzung von Reaktionsbarrieren. Um diesen | 54 | f\u00fcr die Untersch\u00e4tzung von Reaktionsbarrieren. Um diesen | ||
55 | Fehler zu korrigieren, der aus der Untersch\u00e4tzung der | 55 | Fehler zu korrigieren, der aus der Untersch\u00e4tzung der | ||
56 | kurzreichweitigen Pauli Repulsion in DFTB3 resultiert, wurde die | 56 | kurzreichweitigen Pauli Repulsion in DFTB3 resultiert, wurde die | ||
57 | empirische Delta-Pauli Korrektur entwickelt. Allerdings gab es bisher | 57 | empirische Delta-Pauli Korrektur entwickelt. Allerdings gab es bisher | ||
58 | keine Parameter f\u00fcr dieses Model. Daher wurde in dieser Arbeit | 58 | keine Parameter f\u00fcr dieses Model. Daher wurde in dieser Arbeit | ||
59 | der erste Parametersatz f\u00fcr CHNO-basierte Molek\u00fclsysteme | 59 | der erste Parametersatz f\u00fcr CHNO-basierte Molek\u00fclsysteme | ||
60 | entworfen und an relevanten organischen/biochemischen Systemen | 60 | entworfen und an relevanten organischen/biochemischen Systemen | ||
61 | evaluiert. Die Ergebnisse zeigen, dass Delta-Pauli erfolgreich | 61 | evaluiert. Die Ergebnisse zeigen, dass Delta-Pauli erfolgreich | ||
62 | kurzreichweitige Pauli Repulsion in DFTB3 einf\u00fchrt. Dies hat zur | 62 | kurzreichweitige Pauli Repulsion in DFTB3 einf\u00fchrt. Dies hat zur | ||
63 | Folge, dass Delta-Pauli die Beschreibung von Molek\u00fclsystemen | 63 | Folge, dass Delta-Pauli die Beschreibung von Molek\u00fclsystemen | ||
64 | bez\u00fcglich nichtkovalenter Wechselwirkungen, inter- und | 64 | bez\u00fcglich nichtkovalenter Wechselwirkungen, inter- und | ||
65 | intramolekularen Reaktionsbarrieren und Gleichgewichtsgeometrien | 65 | intramolekularen Reaktionsbarrieren und Gleichgewichtsgeometrien | ||
66 | verbessert.\r\nAbstract: The archaeal proton pump bacteriorhodopsin | 66 | verbessert.\r\nAbstract: The archaeal proton pump bacteriorhodopsin | ||
67 | uses sunlight to build up a proton gradient across the cell membrane. | 67 | uses sunlight to build up a proton gradient across the cell membrane. | ||
68 | The mechanism of energy conversion is based on a well investigated | 68 | The mechanism of energy conversion is based on a well investigated | ||
69 | photocycle. Despite over 45 years of research on this bioenergetical | 69 | photocycle. Despite over 45 years of research on this bioenergetical | ||
70 | model system, there is still little information available about the | 70 | model system, there is still little information available about the | ||
71 | last step of the photocycle: the O\u2192ground (bR) state transition. | 71 | last step of the photocycle: the O\u2192ground (bR) state transition. | ||
72 | It is merely assumed that a long-range proton transfer recovers the bR | 72 | It is merely assumed that a long-range proton transfer recovers the bR | ||
73 | state of bacteriorhodopsin. This work aims to shed further light on | 73 | state of bacteriorhodopsin. This work aims to shed further light on | ||
74 | the mechanistic details and thermodynamic/kinetic features of the | 74 | the mechanistic details and thermodynamic/kinetic features of the | ||
75 | O\u2192bR transition. In order to achieve this, computational methods | 75 | O\u2192bR transition. In order to achieve this, computational methods | ||
76 | were used as a viable complement to the experiment since the handling | 76 | were used as a viable complement to the experiment since the handling | ||
77 | of membrane proteins and the targeted objectives pose a quite involved | 77 | of membrane proteins and the targeted objectives pose a quite involved | ||
78 | task to experimental techniques. Initially, structural models for the | 78 | task to experimental techniques. Initially, structural models for the | ||
79 | O, bR and the O* intermediate state were obtained by employing | 79 | O, bR and the O* intermediate state were obtained by employing | ||
80 | enhanced sampling molecular dynamics simulations. For the simulation | 80 | enhanced sampling molecular dynamics simulations. For the simulation | ||
81 | of the (long- range) proton transfer reactions, a hybrid QM/MM setup | 81 | of the (long- range) proton transfer reactions, a hybrid QM/MM setup | ||
82 | based on the semiempirical quantum chemistry method DFTB3 and the | 82 | based on the semiempirical quantum chemistry method DFTB3 and the | ||
83 | CHARMM36 force field was used. The change of Gibbs free energy | 83 | CHARMM36 force field was used. The change of Gibbs free energy | ||
84 | associated with the proton transfer was resolved by employing free | 84 | associated with the proton transfer was resolved by employing free | ||
85 | energy techniques with an advanced reaction coordinate based on the | 85 | energy techniques with an advanced reaction coordinate based on the | ||
86 | center of excess charge representation. The results indicate that the | 86 | center of excess charge representation. The results indicate that the | ||
87 | O\u2192bR conversion represents a slightly exergonic process in which | 87 | O\u2192bR conversion represents a slightly exergonic process in which | ||
88 | the O* state constitutes a metastable intermediate. Concerning the | 88 | the O* state constitutes a metastable intermediate. Concerning the | ||
89 | proton transfer pathway, an interesting finding was made: The | 89 | proton transfer pathway, an interesting finding was made: The | ||
90 | long-range proton transfer is accomplished via a proton hole/in- verse | 90 | long-range proton transfer is accomplished via a proton hole/in- verse | ||
91 | Grotthuss mechanism. Moreover, this charge transfer is accompanied by | 91 | Grotthuss mechanism. Moreover, this charge transfer is accompanied by | ||
92 | the reorientation of a functionally important, positively charged | 92 | the reorientation of a functionally important, positively charged | ||
93 | arginine side chain as well as by the formation of the proton release | 93 | arginine side chain as well as by the formation of the proton release | ||
94 | group. In the course of these studies, DFTB3 was furthermore | 94 | group. In the course of these studies, DFTB3 was furthermore | ||
95 | benchmarked for proton transfer reactions. The method proved to be | 95 | benchmarked for proton transfer reactions. The method proved to be | ||
96 | efficient for the description of these reactions with a small tendency | 96 | efficient for the description of these reactions with a small tendency | ||
97 | to underestimate reaction barriers. In order to correct for this | 97 | to underestimate reaction barriers. In order to correct for this | ||
98 | error, which results from missing short-range Pauli repulsion in | 98 | error, which results from missing short-range Pauli repulsion in | ||
99 | DFTB3, the empirical Delta-Pauli correction was developed. However, | 99 | DFTB3, the empirical Delta-Pauli correction was developed. However, | ||
100 | until now, there were no parameters available for this model. Hence, | 100 | until now, there were no parameters available for this model. Hence, | ||
101 | in this work the first parameter set for CHNO-based molecular systems | 101 | in this work the first parameter set for CHNO-based molecular systems | ||
102 | was derived and benchmarked on relevant organic/biomolecular systems. | 102 | was derived and benchmarked on relevant organic/biomolecular systems. | ||
103 | The results show that Delta-Pauli successfully introduces short-range | 103 | The results show that Delta-Pauli successfully introduces short-range | ||
104 | Pauli repulsion to DFTB3. As a consequence, Delta-Pauli improves the | 104 | Pauli repulsion to DFTB3. As a consequence, Delta-Pauli improves the | ||
105 | description of molecular systems regarding non-covalent interactions, | 105 | description of molecular systems regarding non-covalent interactions, | ||
106 | inter- as well as intramolecular reaction barriers and equilibrium | 106 | inter- as well as intramolecular reaction barriers and equilibrium | ||
107 | geometries.\r\nTechnicalRemarks: see README.pdf", | 107 | geometries.\r\nTechnicalRemarks: see README.pdf", | ||
108 | "num_resources": 0, | 108 | "num_resources": 0, | ||
109 | "num_tags": 24, | 109 | "num_tags": 24, | ||
110 | "orcid": "", | 110 | "orcid": "", | ||
111 | "organization": { | 111 | "organization": { | ||
112 | "approval_status": "approved", | 112 | "approval_status": "approved", | ||
113 | "created": "2023-01-12T13:30:23.238233", | 113 | "created": "2023-01-12T13:30:23.238233", | ||
114 | "description": "RADAR (Research Data Repository) is a | 114 | "description": "RADAR (Research Data Repository) is a | ||
115 | cross-disciplinary repository for archiving and publishing research | 115 | cross-disciplinary repository for archiving and publishing research | ||
116 | data from completed scientific studies and projects. The focus is on | 116 | data from completed scientific studies and projects. The focus is on | ||
117 | research data from subjects that do not yet have their own | 117 | research data from subjects that do not yet have their own | ||
118 | discipline-specific infrastructures for research data management. ", | 118 | discipline-specific infrastructures for research data management. ", | ||
119 | "id": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | 119 | "id": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | ||
120 | "image_url": "radar-logo.svg", | 120 | "image_url": "radar-logo.svg", | ||
121 | "is_organization": true, | 121 | "is_organization": true, | ||
122 | "name": "radar", | 122 | "name": "radar", | ||
123 | "state": "active", | 123 | "state": "active", | ||
124 | "title": "RADAR", | 124 | "title": "RADAR", | ||
125 | "type": "organization" | 125 | "type": "organization" | ||
126 | }, | 126 | }, | ||
127 | "owner_org": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | 127 | "owner_org": "013c89a9-383c-4200-8baa-0f78bf1d91f9", | ||
128 | "private": false, | 128 | "private": false, | ||
129 | "production_year": "2018", | 129 | "production_year": "2018", | ||
130 | "publication_year": "2023", | 130 | "publication_year": "2023", | ||
131 | "publishers": [ | 131 | "publishers": [ | ||
132 | { | 132 | { | ||
133 | "publisher": "Karlsruhe Institute of Technology" | 133 | "publisher": "Karlsruhe Institute of Technology" | ||
134 | } | 134 | } | ||
135 | ], | 135 | ], | ||
136 | "relationships_as_object": [], | 136 | "relationships_as_object": [], | ||
137 | "relationships_as_subject": [], | 137 | "relationships_as_subject": [], | ||
138 | "repository_name": "RADAR (Research Data Repository)", | 138 | "repository_name": "RADAR (Research Data Repository)", | ||
139 | "resources": [], | 139 | "resources": [], | ||
140 | "services_used_list": "", | 140 | "services_used_list": "", | ||
141 | "source_metadata_created": "2023", | 141 | "source_metadata_created": "2023", | ||
142 | "source_metadata_modified": "", | 142 | "source_metadata_modified": "", | ||
143 | "state": "active", | 143 | "state": "active", | ||
144 | "subject_areas": [ | 144 | "subject_areas": [ | ||
145 | { | 145 | { | ||
146 | "subject_area_additional": "", | 146 | "subject_area_additional": "", | ||
147 | "subject_area_name": "Chemistry" | 147 | "subject_area_name": "Chemistry" | ||
148 | } | 148 | } | ||
149 | ], | 149 | ], | ||
150 | "tags": [ | 150 | "tags": [ | ||
151 | { | 151 | { | ||
152 | "display_name": "Pauli repulsion", | 152 | "display_name": "Pauli repulsion", | ||
153 | "id": "2321c2f8-c18f-4a3f-810a-1be6560592e7", | 153 | "id": "2321c2f8-c18f-4a3f-810a-1be6560592e7", | ||
154 | "name": "Pauli repulsion", | 154 | "name": "Pauli repulsion", | ||
155 | "state": "active", | 155 | "state": "active", | ||
156 | "vocabulary_id": null | 156 | "vocabulary_id": null | ||
157 | }, | 157 | }, | ||
158 | { | 158 | { | ||
159 | "display_name": "bacteriorhodopsin", | 159 | "display_name": "bacteriorhodopsin", | ||
160 | "id": "06ee9a49-f2f2-4189-b760-210dbe885c6e", | 160 | "id": "06ee9a49-f2f2-4189-b760-210dbe885c6e", | ||
161 | "name": "bacteriorhodopsin", | 161 | "name": "bacteriorhodopsin", | ||
162 | "state": "active", | 162 | "state": "active", | ||
163 | "vocabulary_id": null | 163 | "vocabulary_id": null | ||
164 | }, | 164 | }, | ||
165 | { | 165 | { | ||
166 | "display_name": "center of excess charge", | 166 | "display_name": "center of excess charge", | ||
167 | "id": "dba3b8a1-6857-45d0-86a8-194389ec1521", | 167 | "id": "dba3b8a1-6857-45d0-86a8-194389ec1521", | ||
168 | "name": "center of excess charge", | 168 | "name": "center of excess charge", | ||
169 | "state": "active", | 169 | "state": "active", | ||
170 | "vocabulary_id": null | 170 | "vocabulary_id": null | ||
171 | }, | 171 | }, | ||
172 | { | 172 | { | ||
173 | "display_name": "density functional tight binding", | 173 | "display_name": "density functional tight binding", | ||
174 | "id": "55eb178e-fd6d-4f5b-8f46-2f0d11376209", | 174 | "id": "55eb178e-fd6d-4f5b-8f46-2f0d11376209", | ||
175 | "name": "density functional tight binding", | 175 | "name": "density functional tight binding", | ||
176 | "state": "active", | 176 | "state": "active", | ||
177 | "vocabulary_id": null | 177 | "vocabulary_id": null | ||
178 | }, | 178 | }, | ||
179 | { | 179 | { | ||
180 | "display_name": "dftb", | 180 | "display_name": "dftb", | ||
181 | "id": "8115d1a7-b8d4-4f33-ba6d-8ee16516b836", | 181 | "id": "8115d1a7-b8d4-4f33-ba6d-8ee16516b836", | ||
182 | "name": "dftb", | 182 | "name": "dftb", | ||
183 | "state": "active", | 183 | "state": "active", | ||
184 | "vocabulary_id": null | 184 | "vocabulary_id": null | ||
185 | }, | 185 | }, | ||
186 | { | 186 | { | ||
187 | "display_name": "dispersion", | 187 | "display_name": "dispersion", | ||
188 | "id": "88cb7954-bbb6-403c-b4ef-8616462654dd", | 188 | "id": "88cb7954-bbb6-403c-b4ef-8616462654dd", | ||
189 | "name": "dispersion", | 189 | "name": "dispersion", | ||
190 | "state": "active", | 190 | "state": "active", | ||
191 | "vocabulary_id": null | 191 | "vocabulary_id": null | ||
192 | }, | 192 | }, | ||
193 | { | 193 | { | ||
194 | "display_name": "enhanced sampling", | 194 | "display_name": "enhanced sampling", | ||
195 | "id": "1640ef19-c03d-4db1-b16b-ad40e764f01d", | 195 | "id": "1640ef19-c03d-4db1-b16b-ad40e764f01d", | ||
196 | "name": "enhanced sampling", | 196 | "name": "enhanced sampling", | ||
197 | "state": "active", | 197 | "state": "active", | ||
198 | "vocabulary_id": null | 198 | "vocabulary_id": null | ||
199 | }, | 199 | }, | ||
200 | { | 200 | { | ||
201 | "display_name": "free energy simulations", | 201 | "display_name": "free energy simulations", | ||
202 | "id": "ba89a1b2-2f0a-4aef-8bc2-8cc67d0029ed", | 202 | "id": "ba89a1b2-2f0a-4aef-8bc2-8cc67d0029ed", | ||
203 | "name": "free energy simulations", | 203 | "name": "free energy simulations", | ||
204 | "state": "active", | 204 | "state": "active", | ||
205 | "vocabulary_id": null | 205 | "vocabulary_id": null | ||
206 | }, | 206 | }, | ||
207 | { | 207 | { | ||
208 | "display_name": "grotthuss mechanism", | 208 | "display_name": "grotthuss mechanism", | ||
209 | "id": "feb46919-4871-4546-b255-e7c22c0ae8b1", | 209 | "id": "feb46919-4871-4546-b255-e7c22c0ae8b1", | ||
210 | "name": "grotthuss mechanism", | 210 | "name": "grotthuss mechanism", | ||
211 | "state": "active", | 211 | "state": "active", | ||
212 | "vocabulary_id": null | 212 | "vocabulary_id": null | ||
213 | }, | 213 | }, | ||
214 | { | 214 | { | ||
215 | "display_name": "hamiltonian replica exchange", | 215 | "display_name": "hamiltonian replica exchange", | ||
216 | "id": "ff704542-6841-496f-86b3-64362d022901", | 216 | "id": "ff704542-6841-496f-86b3-64362d022901", | ||
217 | "name": "hamiltonian replica exchange", | 217 | "name": "hamiltonian replica exchange", | ||
218 | "state": "active", | 218 | "state": "active", | ||
219 | "vocabulary_id": null | 219 | "vocabulary_id": null | ||
220 | }, | 220 | }, | ||
221 | { | 221 | { | ||
222 | "display_name": "hybrid QM-MM simulations", | 222 | "display_name": "hybrid QM-MM simulations", | ||
223 | "id": "77389d34-4484-4c56-bdbf-056aed289355", | 223 | "id": "77389d34-4484-4c56-bdbf-056aed289355", | ||
224 | "name": "hybrid QM-MM simulations", | 224 | "name": "hybrid QM-MM simulations", | ||
225 | "state": "active", | 225 | "state": "active", | ||
226 | "vocabulary_id": null | 226 | "vocabulary_id": null | ||
227 | }, | 227 | }, | ||
228 | { | 228 | { | ||
229 | "display_name": "hydronium", | 229 | "display_name": "hydronium", | ||
230 | "id": "025374f5-e57d-4aa8-b009-18a27f1f8658", | 230 | "id": "025374f5-e57d-4aa8-b009-18a27f1f8658", | ||
231 | "name": "hydronium", | 231 | "name": "hydronium", | ||
232 | "state": "active", | 232 | "state": "active", | ||
233 | "vocabulary_id": null | 233 | "vocabulary_id": null | ||
234 | }, | 234 | }, | ||
235 | { | 235 | { | ||
236 | "display_name": "lc-dftb", | 236 | "display_name": "lc-dftb", | ||
237 | "id": "96fe7d4e-813c-4e18-8f09-113b3b7129cd", | 237 | "id": "96fe7d4e-813c-4e18-8f09-113b3b7129cd", | ||
238 | "name": "lc-dftb", | 238 | "name": "lc-dftb", | ||
239 | "state": "active", | 239 | "state": "active", | ||
240 | "vocabulary_id": null | 240 | "vocabulary_id": null | ||
241 | }, | 241 | }, | ||
242 | { | 242 | { | ||
243 | "display_name": "long-range corrected density functional tight | 243 | "display_name": "long-range corrected density functional tight | ||
244 | binding", | 244 | binding", | ||
245 | "id": "eb899e99-fdd4-4e3a-be61-33676bff2704", | 245 | "id": "eb899e99-fdd4-4e3a-be61-33676bff2704", | ||
246 | "name": "long-range corrected density functional tight binding", | 246 | "name": "long-range corrected density functional tight binding", | ||
247 | "state": "active", | 247 | "state": "active", | ||
248 | "vocabulary_id": null | 248 | "vocabulary_id": null | ||
249 | }, | 249 | }, | ||
250 | { | 250 | { | ||
251 | "display_name": "metadynamics", | 251 | "display_name": "metadynamics", | ||
252 | "id": "0154510a-4d5a-491c-915f-cf5db408014a", | 252 | "id": "0154510a-4d5a-491c-915f-cf5db408014a", | ||
253 | "name": "metadynamics", | 253 | "name": "metadynamics", | ||
254 | "state": "active", | 254 | "state": "active", | ||
255 | "vocabulary_id": null | 255 | "vocabulary_id": null | ||
256 | }, | 256 | }, | ||
257 | { | 257 | { | ||
258 | "display_name": "molecular dynamics simulations", | 258 | "display_name": "molecular dynamics simulations", | ||
259 | "id": "6da00b06-c8e3-4dac-9537-045d61324da6", | 259 | "id": "6da00b06-c8e3-4dac-9537-045d61324da6", | ||
260 | "name": "molecular dynamics simulations", | 260 | "name": "molecular dynamics simulations", | ||
261 | "state": "active", | 261 | "state": "active", | ||
262 | "vocabulary_id": null | 262 | "vocabulary_id": null | ||
263 | }, | 263 | }, | ||
264 | { | 264 | { | ||
265 | "display_name": "molecular mechanics", | 265 | "display_name": "molecular mechanics", | ||
266 | "id": "43a935db-3278-4217-9278-c4e7b7ea0074", | 266 | "id": "43a935db-3278-4217-9278-c4e7b7ea0074", | ||
267 | "name": "molecular mechanics", | 267 | "name": "molecular mechanics", | ||
268 | "state": "active", | 268 | "state": "active", | ||
269 | "vocabulary_id": null | 269 | "vocabulary_id": null | ||
270 | }, | 270 | }, | ||
271 | { | 271 | { | ||
272 | "display_name": "non-covalent interactions", | 272 | "display_name": "non-covalent interactions", | ||
273 | "id": "ad7e0881-bcb8-44fd-9360-8a9ed20f9378", | 273 | "id": "ad7e0881-bcb8-44fd-9360-8a9ed20f9378", | ||
274 | "name": "non-covalent interactions", | 274 | "name": "non-covalent interactions", | ||
275 | "state": "active", | 275 | "state": "active", | ||
276 | "vocabulary_id": null | 276 | "vocabulary_id": null | ||
277 | }, | 277 | }, | ||
278 | { | 278 | { | ||
279 | "display_name": "proton hole", | 279 | "display_name": "proton hole", | ||
280 | "id": "83a5d1c7-88f2-44c2-ba75-f8c1ceb0799a", | 280 | "id": "83a5d1c7-88f2-44c2-ba75-f8c1ceb0799a", | ||
281 | "name": "proton hole", | 281 | "name": "proton hole", | ||
282 | "state": "active", | 282 | "state": "active", | ||
283 | "vocabulary_id": null | 283 | "vocabulary_id": null | ||
284 | }, | 284 | }, | ||
285 | { | 285 | { | ||
286 | "display_name": "proton pump", | 286 | "display_name": "proton pump", | ||
287 | "id": "58c25075-043a-4417-a442-d3ba8a77f1ae", | 287 | "id": "58c25075-043a-4417-a442-d3ba8a77f1ae", | ||
288 | "name": "proton pump", | 288 | "name": "proton pump", | ||
289 | "state": "active", | 289 | "state": "active", | ||
290 | "vocabulary_id": null | 290 | "vocabulary_id": null | ||
291 | }, | 291 | }, | ||
292 | { | 292 | { | ||
293 | "display_name": "proton transfer reactions", | 293 | "display_name": "proton transfer reactions", | ||
294 | "id": "38d43a80-5a50-4717-9629-6969d77db835", | 294 | "id": "38d43a80-5a50-4717-9629-6969d77db835", | ||
295 | "name": "proton transfer reactions", | 295 | "name": "proton transfer reactions", | ||
296 | "state": "active", | 296 | "state": "active", | ||
297 | "vocabulary_id": null | 297 | "vocabulary_id": null | ||
298 | }, | 298 | }, | ||
299 | { | 299 | { | ||
300 | "display_name": "reaction coordinates", | 300 | "display_name": "reaction coordinates", | ||
301 | "id": "b74d98b4-7501-4864-9ffa-869f3c0457ff", | 301 | "id": "b74d98b4-7501-4864-9ffa-869f3c0457ff", | ||
302 | "name": "reaction coordinates", | 302 | "name": "reaction coordinates", | ||
303 | "state": "active", | 303 | "state": "active", | ||
304 | "vocabulary_id": null | 304 | "vocabulary_id": null | ||
305 | }, | 305 | }, | ||
306 | { | 306 | { | ||
307 | "display_name": "rotational barriers", | 307 | "display_name": "rotational barriers", | ||
308 | "id": "8e144f77-739d-43db-95d0-1e0df6b798b6", | 308 | "id": "8e144f77-739d-43db-95d0-1e0df6b798b6", | ||
309 | "name": "rotational barriers", | 309 | "name": "rotational barriers", | ||
310 | "state": "active", | 310 | "state": "active", | ||
311 | "vocabulary_id": null | 311 | "vocabulary_id": null | ||
312 | }, | 312 | }, | ||
313 | { | 313 | { | ||
314 | "display_name": "umbrella sampling", | 314 | "display_name": "umbrella sampling", | ||
315 | "id": "eccfb9a5-ed43-475a-a3a6-494826970a2a", | 315 | "id": "eccfb9a5-ed43-475a-a3a6-494826970a2a", | ||
316 | "name": "umbrella sampling", | 316 | "name": "umbrella sampling", | ||
317 | "state": "active", | 317 | "state": "active", | ||
318 | "vocabulary_id": null | 318 | "vocabulary_id": null | ||
319 | } | 319 | } | ||
320 | ], | 320 | ], | ||
321 | "title": "Simulation of long-range proton transfer - development and | 321 | "title": "Simulation of long-range proton transfer - development and | ||
322 | application", | 322 | application", | ||
323 | "type": "vdataset", | 323 | "type": "vdataset", | ||
324 | "url": "https://doi.org/10.35097/1132" | 324 | "url": "https://doi.org/10.35097/1132" | ||
325 | } | 325 | } |