bluuebunny/crossref_metadata_2025 huggingface dataset:
AFRICAN AMPHORAE IN BOSPOROS (KERCH)
Authors: Смокотина А.В.
Published: October 2023

В ходе археологических исследований в Босфорском переулке г. Керчи в 2007–2009 гг. были выявлены фрагменты африканских амфор, поступавших в г. Боспор непрерывно с первой половины V до первой половины VI вв. Преобладает импорт из двух основных центров (почти 40 %): мастерских на юге провинции Бизацена (Маджура, Унка) (Keay 8B), а также мастерской Сиди Захруни в районе города Набуля в провинции Зевгитана (spatheion 1, Keay 55А, Keay 57В и некоторые другие).

The archaeological excavations in Bosporos Lane in the town of Kerch con ducted in 2007–2009 revealed fragments of African amphorae that were continuously supplied to the town of Bosporus from the first half of the 5th century to the first half of the 6th century. The imported amphorae came from two main centers (almost 40 %), i. e. the workshops in the south of the Byzacena province (Majoura and Iunca) (Keay 8B) and the Sidi Zahruni workshop near the town of Nabeul in the Zeugitana province (spatheion 1, Keay 55А, Keay 57В and some others).
THE BURIAL OF HORSE WARRIOR AT THE SALTOVO-MAYAKI SETTLEMENT OF OTUZY 2 IN SOUTHEASTERN CRIMEA
Authors: Майко В.В. , Набоков А.И.
Published: October 2023

Изучение погребений на территории салтово-маяцких поселенческих комплексов – одна из интереснейших проблем отечественного хазароведения. До сего дня единичные захоронения, зафиксированные на салтовских поселениях Керченского полуострова, в Подонье и Приазовье, по мнению специалистов, были связаны с ритуальной практикой. В пользу этого свидетельствовали и факты обезвреживания погребенного и повторное проникновение в могилу. В 2021 г. при охранных раскопках поселения Отузы 2 в юго-восточном Крыму было открыто уникальное погребение воина-всадника, которое и стало предметом данной ста тьи. Стратиграфические наблюдения и погребальный инвентарь позволяют датировать погребение не ранее первой половины Х в. Этот инвентарь включает все основные элементы салтовских воинских захоронений. Присутствуют и вещи, уникальные для данной категории могил. Некоторые аналогии погребальному инвентарю известны и в захоронениях печенегов. Несмотря на отдельные общие черты, сам погребальный обряд не имеет аналогов не только на территории Таврики, но и за ее пределами. Это пока единственное воинское погребение в материалах всех изученных поселенческих салтовских памятников полуострова. Не исключено, что это захоронение может стать важным источником для выяснения времени и механизма прекращения функционирования салтово-маяцкой культуры Крыма.

The investigation of burials at the Saltovo-Mayatsk settlement complexes is one of the most interesting aspects of Russian Khazar studies. The experts believe that until recently single graves recorded at the Saltovo settlement on the Kerch peninsula, in the Don region and the Pryazovia region were related to ritual practice. The evidence suggests a deconstruction of the body to separate the world of the living from the world of the dead and protect the living from the buried and re-entering the grave. In 2021 the rescue excavations at Otuzy 2 in southeastern Crimea discovered a unique grave of a horse warrior was discovered which is described in this paper. Methods of comparative archaeological analysis and correlation of grave goods date the burial not before the first half of the 10th century. The funerary offerings include all key elements of the Saltovo warrior graves. They also contain some goods unique for this category of the burials. Some analogues to the funerary gifts are known in the burials of the Pechenegs. Despite some com mon features, the funerary rite has no analogues either in Taurica or outside it. So far, it is the only warrior burial among all investigated Saltovo settlement sites on the peninsula. 166 КСИА. Вып. 271. 2023 г. We cannot rule out that this grave can become an important source for clarifying the time when the Saltovo-Mayatsk culture ceased to exist in Crimea and understanding how it happened.
THE CHRISTIAN TOMBSTONE FROM THE BYZANTINE SITE OF GORZUVITA (SOUTHERN COAST OF CRIMEA)
Authors: Евдокимова А.А. , Мастыкова А.В. , Свойский Ю.М.
Published: October 2023

Рассматривается фрагмент каменного надгробия с надписью, найденного в 2018 г. на византийском памятнике Горзувиты, расположенного на территории МДц «Артек» (Южный берег Крыма). Благодаря визуальному изучению находки удалось прочитать текст и установить, что это христианское надгробие. Для получения более надежного прочтения надписи была построена трехмерная полигональная модель фрагмента надгробия с применением алгоритма визуализации геометрии поверхности, использование которого дало возможность скорректировать первоначальное чтение. Совокупность полученных палеографических, археологических и лингвистических данных позволила прочитать поминальную надпись «[Κ(ύρι)ε или (Ι(ησου)ς Χ(ριστο)ς), ἀ]νάπ[αυσον τὸν] δο[ῦλον σοῦ/ τοῦ Θεοῦ/ Χριστοῦ]» – «[Гос поди], помяни раба [Божьего (имя покойного)]» и отнести ее к VI–VII вв.

The paper examines a fragment of an inscribed tombstone found at the Byz antine site of Gorzuvita located in the Artek international children’s center (Southern Coast 197 А. А. Евдокимов а и др. of Crimea) in 2018. By visual examination of the find, the inscription was read and the tombstone was identified as Christian. To ensure a more reliable interpretation of the inscription, a polygonal 3D model of the tombstone fragment was developed employing a geometry-based visualization of the surface which made it possible to correct the initial reading. Based on the dataset of the collected paleogeographical, archaeological and linguistic data, the epitaph on the tombstone was read as “[Κ(ύρι)ε or (Ι(ησου)ς Χ(ριστο)ς), ἀ]νάπ[αυσον τὸν] δο[ῦλον σοῦ / τοῦ Θεοῦ / Χριστοῦ]” which means “[Our Lord], think upon the slave [of God (the name of the deceased)]” and was dated to the 6th– 7 th centuries.
ANALYTICAL METHODS FOR STUDYING THE COMPOSITION OF BRONZE AGE METAL ITEMS: ADVANTAGES AND DISADVANTAGES
Authors: Анкушев М.Н. , Артемьев Д.А. , Блинов И.А. , Рассомахин М.А. , Алаева И.П. , Виноградов Н.Б.
Published: October 2023

Для получения достоверной информации о составе древних металлических изделий необходим правильный выбор методов пробоотбора и анализа. В статье приводится сравнение результатов изучения состава 3 металлических изделий различными аналитическими методами: оптико-эмиссионный спектральный анализ, РФА, СЭМ-ЭДС и ЛА-ИСП-МС. Методы показали хорошую сходимость результатов при определении макропримесей (Sn, Fe, Sb, Ni) в меди и бронзах. Наиболее близкие результаты при высокой чувствительности получены при помощи спектрального анализа и ЛА-ИСП-МС. С помощью РФА и ЛА-ИСП-МС сравнивается состав патины и металла 8 изделий. В патине бронзовых артефактов содержание Sn и Sb в 2–5 раза выше, чем в металле; As – до 10 раз выше; Fe в патине может как оставаться на уровне долей процента, так и значительно увеличиваться в несколько десятков раз. Высокие концентрации S, а также Se и Te зафиксированы только в металле изделия, в патине содержание S составляет 0,3–0,8 мас. %. Литофильные элементы, такие как Si, Ca, Mg, Al, Mn, P, в металле практически не содержатся, однако в патине их концентрации выше на несколько порядков. Из-за значительных различий в составе патинированные части изделия могут лишь ограниченно использоваться для интерпретаций результатов анализа. Проба металла при отборе для валовых типов анализа (спектральный, ИСП-МС) не должна быть заражена частицами патины.

To obtain reliable information about the composition of ancient metal products, the correct choice of sampling and analysis methods is necessary. The article compares the results of studying the composition of 3 metal items by various analytical methods: optical emission spectral analysis, XRF, SEM-EDS and LA-ICP-MS. The methods 213 М. Н. Анкуш ев и др. showed good convergence of results in the determination of macroimpurities (Sn, Fe, Sb, Ni) in copper and bronze. The closest results at high sensitivity were obtained using spectral analysis and LA-ICP-MS. Using XRF and LA-ICP-MS, the composition of the patina and metal of 8 items is compared. In the patina of bronze artifacts, the content of Sn and Sb is 2–5 times higher than in metal; As – up to 10 times higher; Fe in the patina can either remain at the level of fractions of a percent, or significantly increase by several tens of times. High concentrations of S, as well as Se and Te, were recorded only in the metal of the item; in the patina, the S content is 0,3–0,8 wt %. Lithophilic elements such as Si, Ca, Mg, Al, Mn, P are practically not contained in the metal, however, their concentration in patina is higher by several orders of magnitude. Due to the significant differences in composition, the patinated parts of the item can only be used to a limited extent for interpreting the results of the analysis. The metal sample taken for bulk types of analysis (optical emission spectral, ICP-MS) should not be contaminated with patina particles.
ARCHAEOMETALLURGICAL APPROACHES TO THE STUDY OF COPPER-ARSENIC ALLOYS OF THE BRONZE AGE
Authors: Богданов С.В.
Published: October 2023

В статье анализируется репрезентативная серия из 109 экспериментов по легированию рафинированной меди минералами мышьяка в натурных условиях и объемах, позволяющих изготовить металлоемкие орудия; литью, отжигу заготовок и их последующей кузнечно-слесарной обработке. Источником мышьяка в экспериментальных медных сплавах служил арсенопирит. Установлено, что медный раствор можно обогатить мышьяковыми лигатурами тремя основными способами: растворение порошка арсенопирита в перегретом расплаве меди путем дразнения (перемешивания) деревянной жердью; совместная тигельная плавка порошка арсенопирита, перекрытого корольками меди и «шубой» из толченого древесного угля; совместная восстановительная плавка минералов меди и арсенопирита. По указанным технологическим схемам можно обогащать растворы меди любыми соединениями мышьяка. Лишь первые два способа позволяют получить сплавы с заданной пропорцией Cu и As, а также средне - и высокомышьяковые соединения. В статье приведены данные приборных замеров фаз плавления экспериментальных образцов мышьяковых сплавов, особенности их физико-химических свойств. Всего изготовлено 17 орудий из низко - и среднемышьяковых (от 1,5 до 5 % As) сплавов, соответствующих типологическим стандартам восточноевропейских культур бронзового века.

The paper analyzes a representative series of 109 experiments on alloying of refined copper with arsenic minerals in full-scale conditions in the amounts sufficient to produce metal-consuming tools, as well as experiments on casting, annealing of blanks, and their subsequent forging and founder work. Arsenopyrite served as a source of arsenic in experimental copper alloys. It was established that the copper solution can be enriched with arsenic ligatures in three main ways: dissolution of arsenopyrite powder in the superheated copper melt by poling (mixing) with a wooden pole; joint crucible melting of arsenopyrite powder overlaid with copper shot and a «coat» of crushed charcoal; joint reduction melting of copper and arsenopyrite minerals. According to these technological schemes, it is possible to enrich copper solutions with any arsenic compounds. Only the first two methods make it possible to obtain alloys with a given proportion of Cu and As, as well as medium - and high-arsenic compounds. This paper presents the data of instrument measurements of the melting phases of experimental samples of arsenic alloys and the features of their physicochemical properties. In total, 17 tools were made from low- and medium-arsenic alloys (from 1,5 to 5 % As) which is consistent with typological standards of East European cultures of the Bronze Age.
X-RAY FLUORESCENCE STUDIES OF THE BRONZE AGE HOARD (NORTH OF THE TARKHANKUT PENINSULA, NORTHWESTERN CRIMEA)
Authors: Смекалова Т.Н. , Антипенко А.В. , Мульд С.А. , Майко Н.Б.
Published: October 2023

В 2015 г. в северной части п-ова Тарханкут в Северо-Западном Крыму, в 2,3 км к северо-западу от северной окраины с. Владимировка (бывш. Бай-Кият) был найден клад металлических изделий, относящихся к эпохе бронзы. В январе 2023 г. было проведено рентгенофлуоресцентное исследование состава сплава орудий, входящих в этот клад. Почти все предметы, за исключением одного, изготовлены из двухкомпонентной мышьяковой бронзы, с небольшим количеством мышьяка (в среднем 1,78 %). Только стержневидное орудие с раскованной верхней частью и заостренной нижней (долото или стамеска) сделано из тройной мышьяково-никелевой бронзы, в которой содержится 3,1 % мышьяка и 1,56 % никеля. Культурно-типологический анализ предметов из клада в совокупности с интерпретацией данных по составу их сплава позволяет отметить близость найденных предметов к кругу вещей майкопско-новосвободненской общности Северного Кавказа и датировать их ранним бронзовым веком. Исходя из датировки и местонахождения клада, можно предположить его принадлежность к ямной или кемиобинской культурам.

In 2015 a hoard of metal tools dating to the Bronze Age was discovered in the northern part of the Tarkhankut Peninsula 2,3 km northwest of the northern outskirts of the village of Vladimirovka (former Bay-Kiyat). In January 2023, an X-ray fluorescence study of the alloy composition of the tools from the hoard was carried out. Almost all items, with the exception of one tool were made of two-component arsenic bronze with a small amount of arsenic (average 1,78 %). Only a rod-shaped tool with a forged upper part and a pointed lower part (chisel or adze) was made of triple arsenic-nickel bronze containing 3,1 % arsenic and 1,56 % nickel. The cultural and typological analysis of objects from the hoard, along with the interpretation of the data on the composition of their alloy suggests that the found items are close to the artifacts of the Maykop-Novosvobodnaya community from the North Caucasus and can be dated to the Early Bronze Age. Based on the dating and location of the hoard, it can be assumed that it can be attributed to the Yamnaya or Kemi-Oba cultures.
THE DEBATE OVER SMOLENSK – THE CITY OF THE KRIVICHS
Authors: Кренке Н.А. , Ганичев К.А. , Ершов И.Н. , Кованцев А.В. , Крылович О.А. , Лопатина О.А. , Моисеенков Г.О. , Раева В.А. , Савинецкий А.Б.
Published: October 2023

В статье представлены материалы новых раскопок на Соборной горе Смоленска. Стратиграфические разрезы шурфов по кромке верхней площадки горы свидетельствуют о том, что здесь существовал оборонительный вал, датированный по археологическим находкам и радиоуглеродным методом в пределах первой половины IX в. Под валом залегает культурный слой, древнейший горизонт которого с керамикой колочинской традиции датируется в интервале IV–VI (VII) вв., а основной комплекс находок относится к (VII) VIII–IX вв., включает керамику и вещи, типичные для смоленско-полоцких длинных курганов. Хозяйство населения опиралось на земледелие и скотоводство, что документируется анализом остеологической коллекции и находками зерен культурных злаков. Предложена интерпретация, согласно которой поселение на Соборной горе являлось летописным Смоленском – градом кривичей.

The paper describes materials from recent excavations on Cathedral Hill in Smolensk. Stratigraphical sections of the test-pits along the fringe of the upper site of the Hill indicate that defensive earthen works dating to the first half of the 9th century based on archaeological finds and the radiocarbon method existed in the Hill. There is an occupation layer under the earthen works, its oldest horizon contains ceramics related with the Kolochin tradition and is dated within the 4th–6th (7th) centuries, whereas the main assemblage of the finds is dated back to the (7th) 8th – 9th centuries and includes ceramics and items typical of Smolensk-Polotsk long kurgans. The economy of the population was based on agriculture and animal husbandry as documented by the analysis of the osteological assemblage and finds of grains of cultivated crops. According to the proposed interpretation, the settlement on Cathedral Hill was the Smolensk city of the Krivichs mentioned in ancient chronicles.
THE FIRST SITE OF THE SUMNAGIN TRADITION IN KOLYMA DATED BY THE 14C METHOD
Authors: Слободин С.Б. , Зеленская А.Ю.
Published: October 2023

В 2018–2020 гг. в ходе работ археологической экспедиции Северо-Восточного комплексного научно-исследовательского института ДВО РАН на Верхней Колыме в Магаданской области был открыт и исследован памятник каменного века Бурхала. Расположен он в гористой местности долины реки Колымы, на перевале высотой более 1000 м. Полученная в результате раскопок на площади 5,5 кв. м и сборов подъемного материала коллекция каменных орудий (около 500 экз.) была идентифицирована как комплекс раннеголоценовой сумнагинской традиции. По древесному углю, извлеченному из культурного слоя вместе с артефактами, был определен радиоуглеродный (14С) возраст стоянки, составляющий 9300 л. н. На данный момент стоянка является первым и пока единственным датированным по 14С несмешанным памятником сумнагинской традиции как в долине реки Колымы, так и в ее бассейне, площадью 643 000 кв. км. Также стоянка Бурхала – это древнейший мезолитический памятник Севера Дальнего Востока (Колымы, Чукотки, Камчатки). Материалы стоянки позволяют поставить точку в ведущейся с начала 1970-х гг. региональной дискуссии по вопросу о status quo сумнагинской, сибердиковской и малтанской культур на Колыме.

In 2018–2020 the archaeological expedition of the North-Eastern Complex Research Institute of the Far Eastern Branch of the Russian Academy of Sciences in th Upper Kolyma in the Magadan region discovered and investigated the Stone Age site of Burkhala. It is located in the mountainous area of the Kolyma river valley in a pass over the mountains at an altitude of more than 1000 m. The lithic tools (around 500 items) collected during the excavations of an area of 5,5 sq. m and as surface materials were identified as an assemblage of the Early Holocene Sumnagin culture. Using charcoal retrieved from the occupation layer together with the artifacts, the radiocarbon age (14C) of the site was determined as 9300 years old. Presently, the site is the first and so far the only unmixed site of the Sumnagin culture dated by the 14C method both in the Kolyma river valley and this river basin covering an area of 643,000 sq. km. Besides, the Burkhala site is the earliest Mesolithic site in the North of the Far East (Kolyma, Chukotka and Kamchatka). The materials of the site help put an end to the regional discussion on the status quo of the Sumnagin, Siberdik and Maltan cultures in Kolyma that has been going on since the 1970s.
Vergleich von Richtlinien zum Entwurf von Radverkehrsanlagen in Deutschland und Norwegen und deren Konsequenzen für Stadt und Verkehr - Eine qualitative Untersuchung relevanter Regelwerke für den Radverkehr in Städten aus Sicht der Planenden und Nutzenden
Authors:   TU Berlin, Fachgebiet integrierte Verkehrsplanung, Fazlic Nedim
Published: October 2023

Die Bedeutung des Radverkehrs in Städten nimmt stetig zu und dieser Trend wird sich aller Voraussicht nach auch auf absehbare Zeit fortsetzen. Dabei stellt sich aus Sicht der Planenden in Deutschland die Frage, ob das System hierzulande für die Verkehrswende geeignet ist. Können wir mit den uns zur Verfügung stehenden Regelwerken und Entscheidungsstrukturen den (Rad-)Verkehr der Zukunft aktiv gestalten? Oder sind unsere Arbeitsgrundlagen vielmehr ein Hindernis auf dem Weg zur Stadt-Mobilität des 21. Jahrhunderts? Um diese Frage zu beantworten wird ein Vergleich der in Deutschland geltenden Regelwerke der gemeinnützig arbeitenden Forschungsgesellschaft für Straßen- und Verkehrswesen mit denen aus Norwegen und der dort für die Regelwerke zuständigen staatlichen Straßen- und Verkehrsbehörde (statens vegvesen) durchgeführt. Im Gegensatz zur deutschen FGSV ist die norwegische Straßen und Verkehrsbehörde Teil der Exekutive und damit gesamtgesellschaftlich legitimiert. Es stellt sich die Frage, welche Auswirkungen sich durch diesen strukturellen Unterschied bei der Erstellung von Regelwerken für Radverkehrsanlagen ergeben.
Mobilitätsmanagement in Deutschland - Eine kritische Bestandsaufnahme
Authors:   TU Berlin, Fachgebiet integrierte Verkehrsplanung, Schwedes Oliver , Sternkopf Benjamin ,   TU Berlin, Fachgebiet integrierte Verkehrsplanung, Rammert Alexander ,   TU Berlin, Fachgebiet integrierte Verkehrsplanung
Published: October 2023

Die Erstauflage des vorliegenden Discussion Papers im Jahr 2016, hat eine große Resonanz erzeigt. Damals bildete es den Auftakt für das vom Bundesministeriums für Bildung und Forschung geförderte Forschungsprojekts „Mobilitätsmanagement in Deutschland. Möglichkeiten und Grenzen verkehrspolitischer Gestaltung am Beispiel Mobilitätsmanagement“. Den Ausgangspunkt für das Projekt bildete die bis heute immer wieder zu vernehmende Klage, dass das Mobilitätsmanagement zwar allseits gewünscht, aber auch nach fünfundzwanzig Jahren nur verhältnismäßig selten praktiziert wird, geschweige denn, dass es einen allgemein anerkannten Planungsansatz im Kanon der etablierten Verkehrsplanung darstellt. Auch wir sind davon überzeugt, dass das Mobilitätsmanagement über das Potential verfügt, drängende aktuelle verkehrspolitische Probleme zu lösen. Allerdings scheint es uns an der Zeit, für eine kritische Bilanz des Mobilitätsmanagements, um die aktuellen Defizite vorbehaltlos zu identifizieren und angemessene Schlussfolgerungen daraus zu ziehen. Dementsprechend haben wir uns zum Ziel gesetzt, die Gründe für die Diskrepanz von Anspruch und Wirklichkeit im Politikfeld Verkehr zu ermitteln, um die Einsichten dafür zu nutzen, zukünftig zu besseren Ergebnissen beim Mobilitätsmanagement zu gelangen. Eine kritische Bilanz des Mobilitätsmanagements in Deutschland kann nicht von denjenigen erwartet werden, die sich seit vielen Jahren für das Thema engagieren und gegen Anfeindungen der etablierten Verkehrsplanung und -politik verteidigen. Die konstruktive Kritik des Mobilitätsmanagements erfordert vielmehr eine gewisse Distanz und die Möglichkeit aus den Schützengräben herauszutreten, um die eigene Verteidigungshaltung zu hinterfragen. Wir verstehen unsere Kritik mithin als eine verkehrswissenschaftliche Verteidigung des Mobilitätsmanagements gegen die normative Überfrachtung durch seine Anbeter. Dementsprechend haben wir uns zum Ziel gesetzt, die Gründe für die Diskrepanz von Anspruch und Wirklichkeit im Politikfeld Verkehr zu ermitteln, um die Einsichten dafür zu nutzen, zukünftig zu besseren Ergebnissen zu gelangen. Nach Abschluss des Forschungsprojekts und unter Berücksichtigung der vielfältigen Hinweise von Kolleginnen und Kollegen aus dem Praxisfeld des Mobilitätsmanagements, für die wir uns ausdrücklich bedanken möchten, nutzen wir die vorliegende Zweitauflage, um unsere Argumentation zu schärfen. Wir freuen uns daher, dass der Arbeitskreis „Mobilitätsmanagement“ der Forschungsgesellschaft für Straßen- und Verkehrswesen unsere Anregungen aufgenommen hat und schon bald mit einer eigenen Publikation zur Etablierung des Themas beitragen möchte.
Trace Fe in alkaline electrolyte governs the OER activity of perovskite LaNiO3 and La2NiO4 via interaction with redox-active surface NiOxHy formed by applied bias.
Authors: Twight Liam , Tonsberg Ally , Samira Samji , Velinkar Kunal , Dumpert Kora , Ou Yinqing , Wang Le , Nikolla Eranda , Boettcher Shannon
Published: October 2023

Accurate description of activity trends among perovskite oxide oxygen evolution catalysts using electronic descriptors requires that the bulk structure of the catalyst is comparable to that of the surface. Few studies have thus far addressed the dynamic nature of the catalyst’s structure during the oxygen evolution reaction (OER) and the consequential implications for rationalization of activity. Here, we use a combination of electrochemical and materials characterization techniques to show the surface reconstruction of LaNiO3 particles, LaNiO3 epitaxial films, and an analogous Ruddlesden-Popper phase, La2NiO4. Small, but characteristic redox features corresponding to Ni redox in amorphous NiOxHy are observed during cyclic voltammetry of these nominally crystalline materials. The size of these redox features grows with prolonged cycling and contributes to an increased surface area as determined from electrochemical impedance spectroscopy (EIS). These observations are consistent with the reconstruction of the crystalline surface into NiOxHy and subsequent activation by adsorption of Fe forming the well-known and extremely active NiFeOxHy OER catalyst.
A Serine Ligation Method Based on Mitsunobu Reaction and O-to-N Acyl Transfer
Authors: So Regina , Felix Braxton , Jalan Ankur , Kopach Michael , Castle Steven
Published: October 2023

A ligation protocol has been developed in which a peptide containing an N-terminal serine is linked via its side-chain alcohol to the C-terminal carboxylate of a second peptide by Mitsunobu esterification. N-Deprotection of the serine and subsequent exposure to a weak amine base triggers O-to-N acyl transfer, delivering the desired ligation product. A unique aspect of this strategy is the use of the C-terminal carboxylate as a nucleophile rather than as an electrophile. As a result, the ligation occurs without evidence of epimerization. A broad scope of C-terminal nucleophiles is tolerated, including proline and hindered beta-branched residues.
“On-the-fly” Crystal: How to reliably and automatically characterize and construct potential energy surfaces
Authors: Aarabi Mahdi , Pandey Ankit , Poirier Bill
Published: October 2023

In this work, the Crystal code, developed previously by the authors to find “holes” as well as legitimate transition states in existing potential energy surface (PES) functions [JPC Lett. 11, 6468 (2020)], is retooled to perform on-the-fly “direct dynamics”-type PES explorations, as well as automatic construction of new PES functions. In all of these contexts, the chief advantage of Crystal over other methods is its ability to globally map the PES, thereby determining the most relevant regions of configuration space quickly and reliably—even when the dimensionality is rather large. Here, Crystal is used to generate a uniformly-spaced grid of density functional theory (DFT) or ab initio points, truncated over the relevant regions, which can then be used to either: (a) hone in precisely on PES features such as minima and transition states, or; (b) create a new PES function automatically, via interpolation. Proof of concept is demonstrated via application to three molecular systems: water (H2O), methane (CH4), and methylene imine (CH2NH).
A High-Throughput Workflow to Analyze Sequence-Conformation Relationships and Explore Hydrophobic Patterning in Disordered Peptoids
Authors: Day Erin C. , Chittari Supraja S. , Cunha Keila C. , Zhao Jianhan , Dodds James N. , Davis Delaney C. , Baker Erin S. , Berlow Rebecca B. , Shea Joan-Emma , Kulkarni Rishikesh U. , Knight Abigail S.
Published: October 2023

Understanding how a macromolecule’s primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. While parameters describing subsets of disordered proteins and synthetic materials have been established, they are often tailored to specific chemical interactions and monomer classes, limiting their broader applicability. To address this gap, we present a high-throughput workflow that implements a versatile colorimetric conformational assay, introduces a semi-automated sequencing protocol using MALDI-MS/MS, and pioneers a data-driven sequence parameterization methodology that integrates into a predictive algorithm. Using a model system consisting of two-component peptidomimetics (20mer peptoids) containing polar glycine and hydrophobic N-butylglycine residues in a one-bead one-compound (OBOC) library, we visually identified nine classifications of conformational disorder. From this library, we identified 122 unique sequences across varied compositions and conformations, and we developed an image analysis tool that ultimately characterized an order of magnitude larger fraction of the complete library. Low-throughput techniques, atomistic simulations and ion mobility spectrometry coupled with liquid chromatography and mass spectrometry separations (LC-IMS-MS) of purified peptoids, yielded quantitative descriptors of the conformational ensembles formed by three compositionally identical sequences selected from the library. Finally, a data-driven technique was developed that exploits ‘motifs’ within the 20mer sequences to inform a gradient-boosted tree machine learning algorithm towards conformation prediction. This multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery and development of advanced materials with precise conformational control.
Unraveling non-uniform strain-induced crystallization near a crack tip in natural rubber
Authors: Urayama Kenji , Mai Thanh-Tam , Yasui Tomohiro , Tanaka Ruito , Masunaga Hiroyasu , Kabe Taizo , Tsunoda Katsuhiko , Sakurai Shinichi
Published: October 2023

Strain-induced crystallization (SIC) in natural rubber near crack tips significantly enhances crack growth resistance, but understanding the interplay between local strain field and crystallization remains challenging due to confined and heterogeneous characteristics. Using micro-scale digital image correlation and scanning wide-angle X-ray diffraction (with a narrow 10 µm square beam), this study maps local strain tensor properties and SIC in the vicinity of the crack tip and its peripheral zone (approximately 3 x 1 mm area). The analysis reveals a significant correlation between these properties, with the spatial distribution of the local principal strain axis influencing crystal orientation. Crucially, the maximum tensile component in the tensor of local principal strains predominantly dictates local crystallinity, irrespective of strain biaxiality. This finding paves the way for predicting crystallinity distribution using solely strain field data, offering valuable insights into the role of SIC in enhancing the crack growth resistance of natural rubber.
Small-occupation density functional correlation energy correction to wavefunction approximations
Authors: Rodríguez-Jiménez José Aarón , Carreras Abel , Casanova David
Published: October 2023

In this work, we introduce a novel hybrid approach, termed WFT-soDFT, designed to seamlessly incorporate DFT correlation into wavefunction ansatzes. This is achieved through a partitioning of the orbital space, distinguishing between large and small natural occupation numbers (NOONs) associated with wavefunction theory (WFT) and DFT correlation, respectively. The method uses a novel criteria for partitioning the orbital space and mapping the electron density in natural orbitals with small occupation with the correlation energy of fast electrons within the homogeneous electron gas. Central to our approach is the introduction of a separation parameter $\nu$, the choice of the WFT approach, and the correlation functional. Here, we combine the RASCI wavefunction with hole and particle truncation with a local density correlation functional to only account for small-occupation correlation energy. We investigate the performance of the method in the study of small but challenging chemical systems, for which WFT-soDFT demonstrates notable improvements over pristine wavefunction calculations. These findings collectively highlight the potential of the WFT-soDFT approach as a computationally affordable strategy to improve the accuracy of WFT electronic structure calculations.
Two mechanisms for the spontaneous emergence, execution, and reprogramming of chemical logic circuits
Authors: Peng Zhen , Adam Zachary R.
Published: October 2023

A key question in origin-of-life research is how primitive life or life-like systems obtained reusable and reprogrammable machineries of processing information to respond to various environmental and internal stimuli. One strategy to approach this question is viewing living systems as universal chemical computers. This approach focuses upon uncovering how reusable and reprogrammable chemical NOT, AND, and OR logic gates could appear under prebiotically possible scenarios where simple chemicals and second- or lower-order reactions are more frequent than macromolecules and higher-order reactions. Here, we model two theoretical mechanisms of forming Boolean gates based on geochemically plausible reaction systems that could have preceded complex biopolymers. The mechanisms exploit simple bistable autocatalytic systems to encode binary variables and use heterogeneous dilution rates to differentially activate or deactivate autocatalysis in different reactors. We found that NOT, AND, and OR gates, as well as more complex logic circuits, can spontaneously arise from connected, well-mixed flow reactors based on (i) catalysis by a heterodimer between mutually inhibitory autocatalysts or (ii) selectively permeable tunnels connecting reactors. Our results suggest that the prebiotic emergence of chemical logic circuits provides new guides for experimentally actualizing chemical computation.
Automated Quantum Chemistry for Estimating Nucleophilicity and Electrophilicity with Applications to Retrosynthesis and Covalent Inhibitors
Authors: Ree Nicolai , Göller Andreas H. , Jensen Jan H.
Published: October 2023

Reactivity scales such as nucleophilicity and electrophilicity are valuable tools for de- termining chemical reactivity and selectivity. However, prior attempts to predict or calculate nucleophilicity and electrophilicity are either not capable of generalizing well to unseen molecular structures or require substantial computing resources. We present a fully automated quantum chemistry (QM)-based workflow that automatically identi- fies nucleophilic and electrophilic sites and computes methyl cation affinities and methyl anion affinities to quantify nucleophilicity and electrophilicity, respectively. The calcu- lations are based on r2SCAN-3c SMD(DMSO) single-point calculations on GFN1-xTB ALPB(DMSO) geometries that, in turn, derive from a GFNFF-xTB ALPB(DMSO) conformational search. The workflow is validated against both experimental and higher- level QM-derived data resulting in very strong correlations while having a median wall time of less than two minutes per molecule. Additionally, we demonstrate the workflow on two different applications: first, as a general tool for filtering retrosynthetic routes based on chemical selectivity predictions, and second, as a tool for determining the relative reactivity of covalent inhibitors. The code is freely available on GitHub under the MIT open source license and as a web application at www.esnuel.org.
Gaussian Attractive Potential for Carboxylate/Cobalt Surface Interactions
Authors: WU Xiaojing , Steinmann Stephan N. , Michel Carine
Published: October 2023

Ligand-decorated metal surfaces play a pivotal role in various areas of chemistry, particularly in selective catalysis. Molecular dynamics simulations at the molecular mechanics level of theory are best adapted to gain complementary insights to experiments regarding the structure and dynamics of such organic films. However, standard force fields tend to capture only weak physisorption interactions. This is inadequate for ligands that are strongly adsorbed such as carboxylates on metal surfaces. To address this limitation, we employ the Gaussian Lennard-Jones (GLJ) potential, which incorporates an attractive Gaussian potential between the surface and ligand atoms. Here, we develop this approach for the interaction between cobalt surfaces and carboxylate ligands. The accuracy of the GLJ approach is validated through the analysis of the interaction of oxygen with two distinct cobalt surfaces. The accuracy of this method reaches a root mean square deviation (RMSD) of about 3 kcal/mol across all probed configurations, which corresponds to a percentage error of roughly 4%. Application of the GLJ force field to the dynamics of the organic layer on these surfaces reveals how the ligand concentration influences the film order, and highlights differing mobility in the x and y directions, attributable to surface corrugation on Co(1120). GLJ is versatile, suitable for a broad range of metal/ligand systems, and can, subsequently, be utilized to study the organic film on the adsorption/desorption of reactants and products during a catalytic process.
Molecular simulation approaches to study crystal nucleation from solutions: theoretical considerations and computational challenges
Authors: Finney Aaron , Salvalaglio Matteo
Published: October 2023

Nucleation is the initial step towards the formation of crystalline materials from solutions. Various factors, such as environmental conditions, composition, and external fields, can influence its outcomes and rates. Indeed, controlling this rate-determining step towards phase separation can affect the resulting material structure and properties, which are crucial for a range of scientific fields. Atomistic simulations can be exploited to gain insight into nucleation mechanisms - an aspect difficult to ascertain in experiments - and estimate nucleation rates. However, the microscopic nature of simulations affects the phase behaviour of nucleating solutions when compared to macroscale counterparts. An additional challenge is the inadequate timescales accessible to standard molecular simulations to simulate nucleation directly; this is due to the inherent rareness of nucleation events, which may be apparent in silico at even high supersaturations. In recent decades, molecular simulation methods have emerged to circumvent length- and timescale limitations. However, it is not obvious which simulation method is most suitable to study crystal nucleation from solution. This review surveys the recent advances in this field, shedding light on typical nucleation mechanisms and the appropriateness of various simulation techniques for their study. Herein, we aim to provide a deeper understanding of the complexities associated with modelling crystal nucleation from solution and identify areas for further research. Our review targets researchers across various scientific domains, including materials science, chemistry, physics and engineering, and will hopefully foster a collaborative effort to develop new strategies to comprehend and control nucleation.
Artificial nucleotide codons for enzymatic DNA synthesis
Authors: Sabat Nazarii , Stämpfli Andreas , Flamme Marie , Hanlon Steven , Bisagni Serena , Sladojevich Filippo , Püntener Kurt , Hollenstein Marcel
Published: October 2023

Herein, we report the high yielding solid-phase synthesis of unmodified and chemically modified trinucleotide triphosphates (dN3TPs). These synthetic codons can be used for enzymatic DNA synthesis provided their scaffold is stabilized with phosphorothioate units. Enzymatic synthesis with three rather than one letter nucleotides will be useful for the production of xenonucleic acids (XNAs) and for in vitro selection of modified functional nucleic acids.
Anubis: Bayesian optimization with unknown feasibility constraints for scientific experimentation
Authors: Hickman Riley , Aldeghi Matteo , Aspuru-Guzik Alán
Published: October 2023

Model-based optimization strategies, such as Bayesian optimization (BO), have been deployed across the natural sciences in design and discovery campaigns due to their sample efficiency and flexibility. The combination of such strategies with automated laboratory equipment and/or high-performance computing in a suggest-make-measure closed-loop constitutes a self-driving laboratory (SDL), which have been endorsed as a next-generation technology for autonomous scientific experimentation. Despite the promise of early SDL prototypes, a lack of flexible experiment planning algorithms prevents certain prevalent optimization problem types from being addressed. For instance, many experiment planning algorithms are unable to intelligently deal with failed measurements resulting from a priori unknown constraints on the parameter space. Such constraint functions are pervasive in chemistry and materials science research, stemming from unexpected equipment failures, failed/abandoned syntheses, or unstable molecules or materials. In this work, we provide a comprehensive discussion and benchmark of BO strategies to deal with a priori unknown constraints, characterized by learning the constraint function on-the-fly using a variational Gaussian process classifier and combining its predictions with the typical BO regression surrogate to parameterize feasibility-aware acquisition functions. These acquisition functions balance sampling parameter space regions deemed to be promising in terms of optimization objectives with avoidance of regions predicted to be infeasible. In addition to benchmarking feasibility-aware acquisition functions on analytic optimization benchmark surfaces, we conduct two realistic optimization benchmarks derived from previously reported studies: inverse design of hybrid organic-inorganic halide perovskite materials with unknown stability constraints, and the design of BCR-Abl kinase inhibitors with unknown synthetic accessibility constraints. We deliver intuitive recommendations to readers on which strategies work best for various scenarios. Overall, this work contributes to advancing the practicality and efficiency of autonomous experimentation in SDLs. All strategies introduced in this work are implemented as part of the open-source Atlas Python library.
An empirical experimental observations and MD simulation data-based model for the material properties of confined fluids in nano/Angstrom size tubes
Authors: Garg Ashish , Bisnoi Swati
Published: October 2023

The transport of fluids in nanometer and Angstrom-sized pores has gotten much attention because of its potential uses in nanotechnology, energy storage, and healthcare sectors. Understanding the distinct material properties of fluids in such close confinement is critical for enhancing their performance in various applications. These properties dictate the fluid's behavior and play a crucial role in determining flow dynamics, transport processes, and, ultimately, the performance of nanoscale devices. Remarkably, many researchers observed that the size of the geometry, such as the diameter of the confining nanotube, exerts a profound and intriguing influence on the material properties of nanoconfined fluids, including on the critical parameters such as density, viscosity, and slip length. Many researchers tried to model these material properties: viscosity $\eta$, density $\rho$, and slip $\lambda$ using various models with many dependencies on the tube diameter. It is somewhat confusing and tough to decide which model is appropriate and needs to be incorporated in the numerical simulation. In this paper, we tried to propose a simple single equation for each nano confined material property such as for density $\displaystyle \rho(D)/\rho_o = a+ b/(D-c)^n$, viscosity $\displaystyle \eta(D)/\eta_o = a+ b/(D-c)^n$, and the slip length $\lambda(D) = \lambda_1~D~e^{-n~D}+ \lambda_o$ (where $a,~b,~c,~n,~\lambda_1,~\lambda_o$ are the free fitting parameters). We model a wealth of previous experimental and MD simulation data from the literature using our proposed model for each material property of nanoconfined fluids at the nanometer and Angstrom scales. Our single proposed equation effectively captures and models all the data, even though many different models have been employed in the existing literature to describe the same material property. Our proposed model exhibits exceptional agreement with multiple independent datasets from the experimental observations and molecular dynamics simulations. Additionally, the model possesses the advantageous properties of continuity and a continuous derivative, so the proposed model is well-suited for integration into numerical simulations. Further, the proposed models also obey the far boundary conditions, i.e., when tube diameter $D \implies \infty$, the material properties tend to the bulk properties of the fluid. Due to the models' simplicity, smooth, and generic nature, this heuristic model holds promise to apply in simulations to design and optimize nanoscale devices.
TransPTM: a Transformer-Based Model for Non-Histone Acetylation Site Prediction
Authors: Meng Lingkuan , Chen Xingjian , Cheng Ke , Chen Nanjun , Zheng Zetian , Wang Fuzhou , Sun Hongyan , Wong Ka-Chun
Published: October 2023

Protein acetylation is one of the extensively studied post-translational modifications (PTMs) for its sig- nificant roles across a myriad of biological processes. Although many computationl tools for acetylation site identification have been developed, there is a lack of benchmark dataset and bespoke predictors for non-histone acetylation site prediction. To address those problems, we have contributed to both dataset creation and predictor benchmark in this study. Firstly, we construct a non-histone acetylation site bench- mark dataset, namely NHAC, which includes 11 subsets according to the sequence length ranging from 11 to 61 amino acids. There are totally 886 positive samples and 4707 negative samples for each sequence length. Secondly, we propose a transformer-based neural network model, TransPTM, for non-histone acetylation site predication. Our model introduces a pre-trained protein language model ProtT5 to con- struct the site’s feature space. The GNN framewrk consists of three TransformerConv layers for feature extraction and a multilayer perceptron (MLP) module for classification. In experiments, TransPTM has the competitive performance for non-histone acetylation site prediction over 3 SOTA tools. It improves our comprehension on the PTM mechanism and provides a theoretical basis for developing drug targets for diseases. Moreover, the created PTM datasets fills the gap in non-histone acetylation site datasets and is beneficial to the related communities. The source code and data utilized by TransPTM are accessible at https://www.github.com/TransPTM.
Pushing Boundaries in Single Molecule Magnets: An Ab Initio Perspective on Harnessing Unusual Oxidation States for Unprecedented Lanthanide SMM Performance
Authors: Sharma Tanu , Swain Abinash , Rajaraman Gopalan
Published: October 2023

The recent breakthrough of attaining blocking temperature near liquid N2 temperature rekindled the interest in lanthanide-based Single Molecule Magnets towards end-user applications. Within this realm, several challenges are present, with a key objective being the further enhancement of the blocking temperature. As the current set of molecules based on Dy(III) has already reached their maximum potential barrier height for magnetization reversal (Ueff), chemical insights-based developments are hampered. In this connection, using DFT and ab initio CASSCF methods, we have explored the possibility of obtaining lanthanide SMMs in unusual oxidation states such as +4 and +5. We are encouraged by the fact that several such complexes are already reported, with some of them found to exhibit performant SMM characteristics. We begin with various small models of [LnO2], [LnO2]−, and [LnO2]+ (Ln varying from Ce to Lu) systems to correlate the nature of the lanthanides to the SMM characteristics. We have also extended our study to include five complexes reported earlier possessing +4 and +5 oxidation states to offer clues to improve the SMM characteristics. Our calculations reveal several advantages in fine-tuning the oxidation state in lanthanide SMMs, and this includes (i) the lanthanide-ligand covalency found to increase as high as 45% compared to the LnIII counterpart (ii) yield barrier height for magnetization reversal as high as 8500 cm-1, an unprecedented tuning up to three times larger compared to the best-in-class LnIII counterpart (iii) among various ways to stabilise such high-oxidation state including encapsulation yield several targets with HoO2@SWCNT(4,4) predicted to yield an impressive energy barrier of ~5400 cm−1 (iv) the stronger lanthanide-ligand bonds also found to help in tuning the spin-phonon relaxation as stronger bonds found to offset the vibrations that cause the relaxation, potentially yield larger blocking temperatures - offering a never-before-seen strategy to new class lanthanide SMMs.